Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity data An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol http://purl.obolibrary.org/obo/IAO_0000028 symbol CRID symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. http://purl.obolibrary.org/obo/IAO_0000578 centrally registered identifier http://purl.obolibrary.org/obo/IAO_0020000 identifier CRID An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. http://purl.obolibrary.org/obo/IAO_0000579 centrally registered identifier registry http://purl.obolibrary.org/obo/IAO_0020020 code set CRID registry A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. http://purl.obolibrary.org/obo/IAO_0020000 identifier http://purl.obolibrary.org/obo/IAO_0000030 information content entity proper name An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. http://purl.obolibrary.org/obo/IAO_0020010 identifier creating process http://purl.obolibrary.org/obo/OBI_0000011 planned process naming A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. http://purl.obolibrary.org/obo/IAO_0020020 code set http://purl.obolibrary.org/obo/IAO_0000030 information content entity code map An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. http://purl.obolibrary.org/obo/PLANA_0007547 anterior pole progenitor cell http://purl.obolibrary.org/obo/PLANA_0000429 neoblast piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole. http://purl.obolibrary.org/obo/GO_0140013 meiotic nuclear division http://purl.obolibrary.org/obo/GO_1903046 meiotic cell cycle process One of the two nuclear divisions that occur as part of the meiotic cell cycle. http://purl.obolibrary.org/obo/PLANA_0000131 primordium http://purl.obolibrary.org/obo/UBERON_0007567 regenerating anatomical structure Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue. http://purl.obolibrary.org/obo/PLANA_0000133 mechanoreceptor cell http://purl.obolibrary.org/obo/PLANA_0000552 sensory neuron A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. http://purl.obolibrary.org/obo/PLANA_0000201 bursal canal http://purl.obolibrary.org/obo/PLANA_0000113 tissue The passageway connecting the genital atrium to the copulatory bursa. Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the copulatory bursa before travelling up the oviducts to the tuba. http://purl.obolibrary.org/obo/PLANA_0000203 gonopore http://purl.obolibrary.org/obo/PLANA_0002079 pore The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying. http://purl.obolibrary.org/obo/PLANA_0000204 ovary http://purl.obolibrary.org/obo/BFO_0000040 material entity A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development. http://purl.obolibrary.org/obo/PLANA_0000205 oviduct http://purl.obolibrary.org/obo/PLANA_0002089 reproductive organ Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium. http://purl.obolibrary.org/obo/PLANA_0000206 penis papilla http://purl.obolibrary.org/obo/PLANA_0002089 reproductive organ A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal. http://purl.obolibrary.org/obo/PLANA_0000207 sperm duct http://purl.obolibrary.org/obo/PLANA_0002089 reproductive organ A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles. http://purl.obolibrary.org/obo/PLANA_0000208 testis http://purl.obolibrary.org/obo/BFO_0000040 material entity A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration. http://purl.obolibrary.org/obo/PLANA_0000211 primitive ectoderm cell http://purl.obolibrary.org/obo/PLANA_0004518 extraembryonic cell Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2. http://purl.obolibrary.org/obo/PLANA_0000214 juvenile stage http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage A postnatal stage of Smed development that initiates with hatching and proceeds until sexual maturity is reached. Reproductive structures develop during the juvenile stage. http://purl.obolibrary.org/obo/PLANA_0000215 reproductive system product http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules. http://purl.obolibrary.org/obo/PLANA_0000216 egg capsule http://purl.obolibrary.org/obo/PLANA_0000215 reproductive system product A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos.Egg capsules are anchored to a substrate via a stalk. http://purl.obolibrary.org/obo/PLANA_0000217 gonad http://purl.obolibrary.org/obo/PLANA_0002089 reproductive organ Reproductive organ that produces and releases eggs (ovary) or sperm (testis). http://purl.obolibrary.org/obo/PLANA_0000218 male primordial germ cell http://purl.obolibrary.org/obo/PLANA_0000121 stem cell Cells coexpressing piwi-1 and nanos that are required for male gonad formation. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with spermatogonial stem cell. http://purl.obolibrary.org/obo/PLANA_0000219 spermatogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000121 stem cell gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm. http://purl.obolibrary.org/obo/PLANA_0000220 spermatogonium http://purl.obolibrary.org/obo/PLANA_0000120 progenitor cell An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation. http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte http://purl.obolibrary.org/obo/BFO_0000040 material entity A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. http://purl.obolibrary.org/obo/PLANA_0000222 spermatid http://purl.obolibrary.org/obo/BFO_0000040 material entity A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. http://purl.obolibrary.org/obo/PLANA_0000223 oogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000121 stem cell A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes. http://purl.obolibrary.org/obo/PLANA_0000224 cement gland http://purl.obolibrary.org/obo/PLANA_0000113 tissue Glands surrounding the genital atrium that are required for production of the proteinaceous egg capsule shell and stalk. http://purl.obolibrary.org/obo/PLANA_0000227 germ cell http://purl.obolibrary.org/obo/PLANA_0000499 cell 1. A gamete (as an egg or sperm cell) or one of its antecedent cells. 2. A mature male or female germ cell usually possessing a haploid chromosome set and capable of initiating formation of a new diploid individual by fusion with a gamete of the opposite sex. http://purl.obolibrary.org/obo/PLANA_0000228 male germ cell http://purl.obolibrary.org/obo/PLANA_0000227 germ cell A male germ cell is a germ cell that supports male gamete production. http://purl.obolibrary.org/obo/PLANA_0000229 female germ cell http://purl.obolibrary.org/obo/PLANA_0000227 germ cell Female germ cell is a germ cell that supports female gamete production. http://purl.obolibrary.org/obo/PLANA_0000230 tuba http://purl.obolibrary.org/obo/PLANA_0002089 reproductive organ A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct. http://purl.obolibrary.org/obo/PLANA_0000231 vitelline gland http://purl.obolibrary.org/obo/PLANA_0000113 tissue Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules. http://purl.obolibrary.org/obo/PLANA_0000232 copulatory apparatus http://purl.obolibrary.org/obo/PLANA_0002090 reproductive structure Accessory reproductive structures involved in copulation, egg capsule development and laying. http://purl.obolibrary.org/obo/PLANA_0000233 copulatory bursa http://purl.obolibrary.org/obo/PLANA_0002089 reproductive organ An organ that receives and stores sperm from mating partners. http://purl.obolibrary.org/obo/PLANA_0000234 seminal vesicle http://purl.obolibrary.org/obo/PLANA_0002089 reproductive organ Glandular pouches adjoining the sperm ducts which produce seminal fluid. http://purl.obolibrary.org/obo/PLANA_0000237 round spermatid http://purl.obolibrary.org/obo/PLANA_0000222 spermatid A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, andundergo morphogenesis to produce mature sperm. http://purl.obolibrary.org/obo/PLANA_0000238 elongate spermatid http://purl.obolibrary.org/obo/PLANA_0000222 spermatid Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm. http://purl.obolibrary.org/obo/PLANA_0000239 oogonial cell http://purl.obolibrary.org/obo/PLANA_0000120 progenitor cell An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. http://purl.obolibrary.org/obo/PLANA_0000240 body wall musculature http://purl.obolibrary.org/obo/BFO_0000040 material entity Any collection of muscles that is part of a body wall [Automatically generated definition]. http://purl.obolibrary.org/obo/PLANA_0000241 pharynx longitudinal muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell Pharynx muscle fibers running anteroposterior (proximal to distal). http://purl.obolibrary.org/obo/PLANA_0000404 pharynx lumen http://purl.obolibrary.org/obo/PLANA_0002053 lumen Anatomical space enclosed by the pharynx inner epithelium. http://purl.obolibrary.org/obo/PLANA_0000405 digestive tract lumen http://purl.obolibrary.org/obo/PLANA_0002053 lumen An anatomical space that is surrounded by a digestive tract. http://purl.obolibrary.org/obo/PLANA_0000406 oral opening http://purl.obolibrary.org/obo/UBERON_0002553 anatomical cavity The orifice that connects the mouth to the exterior of the body. http://purl.obolibrary.org/obo/PLANA_0000407 pharynx pouch cavity http://purl.obolibrary.org/obo/UBERON_0002553 anatomical cavity Anatomical space between the pharynx and the epithelial cells comprising parapharyngeal pouch. http://purl.obolibrary.org/obo/PLANA_0000409 apical surface of the epidermis http://purl.obolibrary.org/obo/BFO_0000040 material entity The apical surface of the single layered epidermis that is in contact with the environment. http://purl.obolibrary.org/obo/PLANA_0000410 basal surface of the epidermis http://purl.obolibrary.org/obo/BFO_0000040 material entity The basal surface of the epidermis in direct contact with the basal lamina. http://purl.obolibrary.org/obo/PLANA_0000411 gastrodermis surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface The surface of the gastrodermis in contact with the gut lumen. http://purl.obolibrary.org/obo/PLANA_0000412 pharynx inner epithelium surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface The epithelial surface lining the interior of the pharynx, facing the lumen. http://purl.obolibrary.org/obo/PLANA_0000413 pharynx outer epithelium surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface Epithelial surface covering the outside of the pharynx. http://purl.obolibrary.org/obo/PLANA_0000414 pharynx pouch epithelial surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface The surface of the parapharyngeal pouch facing the pharynx. http://purl.obolibrary.org/obo/PLANA_0000417 definitive organism subdivision http://purl.obolibrary.org/obo/UBERON_0000475 organism subdivision Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems. http://purl.obolibrary.org/obo/PLANA_0000418 head region http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region The head is the anterior-most division of the body [GO]. A three dimensional compartment bounded by the anterior margin or the head and the posterior boundary of the cephalic ganglia (brain). http://purl.obolibrary.org/obo/PLANA_0000419 prepharyngeal region http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the pharynx. http://purl.obolibrary.org/obo/PLANA_0000420 parapharyngeal region http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region Region of the animal lateral to and surrounding the pharynx. http://purl.obolibrary.org/obo/PLANA_0000421 tail region http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region Caudal region, beginning at the mouth and ending at posterior pole. http://purl.obolibrary.org/obo/PLANA_0000422 tail stripe http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region Medial region of the tail; the parenchymal space between the posterior primary gut branches. http://purl.obolibrary.org/obo/PLANA_0000423 embryonic subdivision http://purl.obolibrary.org/obo/UBERON_0000475 organism subdivision Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems. http://purl.obolibrary.org/obo/PLANA_0000427 multicellular anatomical structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure An anatomical structure that has more than one cell as a part. http://purl.obolibrary.org/obo/PLANA_0000428 musculature system http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system Total musculature of the planarian body. http://purl.obolibrary.org/obo/PLANA_0000429 neoblast http://purl.obolibrary.org/obo/PLANA_0000121 stem cell A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline. http://purl.obolibrary.org/obo/PLANA_0000430 epithelial cell component http://purl.obolibrary.org/obo/GO_0005575 cellular_component A part of an epithelial cell. http://purl.obolibrary.org/obo/PLANA_0000431 organ http://purl.obolibrary.org/obo/PLANA_0000427 multicellular anatomical structure Anatomical structure that performs a specific function or group of functions. http://purl.obolibrary.org/obo/PLANA_0000459 optic chiasm http://purl.obolibrary.org/obo/BFO_0000040 material entity A decussation of the diencephalon where the fibers of the optic nerve cross http://purl.obolibrary.org/obo/PLANA_0000460 anterior commissure http://purl.obolibrary.org/obo/PLANA_0000494 brain commissure A bundle of nerve fibers connecting the two cephalic ganglia. http://purl.obolibrary.org/obo/PLANA_0000461 lateral branch http://purl.obolibrary.org/obo/PLANA_0000113 tissue Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation. http://purl.obolibrary.org/obo/PLANA_0000462 sensory cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell A cell that performs a sensory function. http://purl.obolibrary.org/obo/PLANA_0000463 cholinergic neuron http://purl.obolibrary.org/obo/BFO_0000004 independent continuant Neurons that express choline acetyltransferase. http://purl.obolibrary.org/obo/PLANA_0000464 GABAergic neuron http://purl.obolibrary.org/obo/BFO_0000004 independent continuant Neurons that express glutamine decarboxylase. http://purl.obolibrary.org/obo/PLANA_0000465 pharynx nerve plexus http://purl.obolibrary.org/obo/BFO_0000040 material entity Plexus of nerves located in the pharynx comprised of inner and outer wall rings. http://purl.obolibrary.org/obo/PLANA_0000466 subepidermal nerve plexus http://purl.obolibrary.org/obo/BFO_0000040 material entity Plexus of nerves located just between the epidermis and the body wall musculature. http://purl.obolibrary.org/obo/PLANA_0000467 submuscular nerve plexus http://purl.obolibrary.org/obo/BFO_0000040 material entity Plexus of nerves that innervate the body wall musculature. http://purl.obolibrary.org/obo/PLANA_0000468 gastrodermal plexus http://purl.obolibrary.org/obo/BFO_0000040 material entity A thin net of single nerve fibers located around the gut. http://purl.obolibrary.org/obo/PLANA_0000470 neuropil http://purl.obolibrary.org/obo/PLANA_0000113 tissue A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur. http://purl.obolibrary.org/obo/PLANA_0000472 pharynx outer epithelium http://purl.obolibrary.org/obo/PLANA_0002023 ciliated epithelium Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft. http://purl.obolibrary.org/obo/PLANA_0000473 pharynx outer circular muscle cell http://purl.obolibrary.org/obo/PLANA_0007535 pharynx circular muscle cell Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles. http://purl.obolibrary.org/obo/PLANA_0000474 pharynx inner circular muscle cell http://purl.obolibrary.org/obo/PLANA_0007535 pharynx circular muscle cell Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers. http://purl.obolibrary.org/obo/PLANA_0000475 pharynx inner longitudinal muscle cell http://purl.obolibrary.org/obo/PLANA_0000241 pharynx longitudinal muscle cell Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface. http://purl.obolibrary.org/obo/PLANA_0000476 pharynx outer longitudinal muscle cell http://purl.obolibrary.org/obo/PLANA_0000241 pharynx longitudinal muscle cell Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium. http://purl.obolibrary.org/obo/PLANA_0000477 pharynx radial muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts. http://purl.obolibrary.org/obo/PLANA_0000478 pharynx musculature http://purl.obolibrary.org/obo/PLANA_0000113 tissue The total musculature within the pharynx. http://purl.obolibrary.org/obo/PLANA_0000479 pharynx inner nerve plexus http://purl.obolibrary.org/obo/PLANA_0000465 pharynx nerve plexus Ring of the pharynx nerve plexus that is proximal to the lumen. http://purl.obolibrary.org/obo/PLANA_0000480 pharynx outer nerve plexus http://purl.obolibrary.org/obo/PLANA_0000465 pharynx nerve plexus Ring of the pharynx nerve plexus that is proximal to the exterior surface. http://purl.obolibrary.org/obo/PLANA_0000481 serotonergic neuron http://purl.obolibrary.org/obo/BFO_0000040 material entity Neurons that express the neurotransmitter serotonin. http://purl.obolibrary.org/obo/PLANA_0000482 dopaminergic neuron http://purl.obolibrary.org/obo/BFO_0000004 independent continuant A neuron that expresses the neurotransmitter dopamine. http://purl.obolibrary.org/obo/PLANA_0000483 octopaminergic neuron http://purl.obolibrary.org/obo/BFO_0000004 independent continuant Neurons that express the biogenic amine octopamine. http://purl.obolibrary.org/obo/PLANA_0000484 secretory system http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus. http://purl.obolibrary.org/obo/PLANA_0000485 gland cell http://purl.obolibrary.org/obo/PLANA_0000100 epithelial cell Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly throughepithelial cells and form a secretory pore at the surface. http://purl.obolibrary.org/obo/PLANA_0000486 secretory pore http://purl.obolibrary.org/obo/PLANA_0002079 pore The opening by which the gland cells secrete mucus to the exterior of the animal. http://purl.obolibrary.org/obo/PLANA_0000487 acidophilic gland cell http://purl.obolibrary.org/obo/PLANA_0000485 gland cell One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsoventral border of the animal. http://purl.obolibrary.org/obo/PLANA_0000488 basophilic gland cell http://purl.obolibrary.org/obo/PLANA_0000485 gland cell One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells. http://purl.obolibrary.org/obo/PLANA_0000492 nerve plexus http://purl.obolibrary.org/obo/PLANA_0000113 tissue Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. http://purl.obolibrary.org/obo/PLANA_0000494 brain commissure http://purl.obolibrary.org/obo/PLANA_0002025 commissure any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain http://purl.obolibrary.org/obo/PLANA_0000495 blastema http://purl.obolibrary.org/obo/UBERON_0007567 regenerating anatomical structure A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise. http://purl.obolibrary.org/obo/PLANA_0000499 cell http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. http://purl.obolibrary.org/obo/PLANA_0000501 cell projection http://purl.obolibrary.org/obo/GO_0005575 cellular_component A prolongation or process extending from a cell. http://purl.obolibrary.org/obo/PLANA_0000502 actin-based cell projection http://purl.obolibrary.org/obo/PLANA_0000501 cell projection A cell projection supported by an assembly of actin filaments. http://purl.obolibrary.org/obo/PLANA_0000504 microvillus http://purl.obolibrary.org/obo/PLANA_0000502 actin-based cell projection Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. http://purl.obolibrary.org/obo/PLANA_0000505 cell-cell contact zone http://purl.obolibrary.org/obo/GO_0005575 cellular_component Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions. http://purl.obolibrary.org/obo/PLANA_0000506 cell junction http://purl.obolibrary.org/obo/PLANA_0000505 cell-cell contact zone A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. http://purl.obolibrary.org/obo/PLANA_0000507 cell-cell junction http://purl.obolibrary.org/obo/PLANA_0000506 cell junction A cell junction that forms a connection between two or more cells in a multicellular organism; this excludes direct cytoplasmic junctions such as ring canals. http://purl.obolibrary.org/obo/PLANA_0000508 cell-cell adhesion http://purl.obolibrary.org/obo/PLANA_0000505 cell-cell contact zone The attachment of one cell to another cell via adhesion molecules. http://purl.obolibrary.org/obo/PLANA_0000509 intracellular part http://purl.obolibrary.org/obo/GO_0005575 cellular_component Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. http://purl.obolibrary.org/obo/PLANA_0000510 cytoplasm http://purl.obolibrary.org/obo/PLANA_0000509 intracellular part All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures http://purl.obolibrary.org/obo/PLANA_0000513 cytoplasmic part http://purl.obolibrary.org/obo/PLANA_0000509 intracellular part Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. http://purl.obolibrary.org/obo/PLANA_0000514 cytoplasmic vesicle part http://purl.obolibrary.org/obo/PLANA_0000513 cytoplasmic part Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. http://purl.obolibrary.org/obo/PLANA_0000515 vacuole http://purl.obolibrary.org/obo/PLANA_0000526 membrane-bounded organelle A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. http://purl.obolibrary.org/obo/PLANA_0000518 intracellular organelle http://purl.obolibrary.org/obo/PLANA_0000509 intracellular part Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. http://purl.obolibrary.org/obo/PLANA_0000519 intracellular non-membrane-bounded organelle http://purl.obolibrary.org/obo/PLANA_0000531 non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes http://purl.obolibrary.org/obo/PLANA_0000520 membrane http://purl.obolibrary.org/obo/GO_0005575 cellular_component A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. http://purl.obolibrary.org/obo/PLANA_0000521 bounding membrane of organelle http://purl.obolibrary.org/obo/PLANA_0000520 membrane Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. http://purl.obolibrary.org/obo/PLANA_0000522 membrane part http://purl.obolibrary.org/obo/GO_0005575 cellular_component Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. http://purl.obolibrary.org/obo/PLANA_0000523 plasma membrane part http://purl.obolibrary.org/obo/PLANA_0000522 membrane part Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. http://purl.obolibrary.org/obo/PLANA_0000524 organelle membrane http://purl.obolibrary.org/obo/PLANA_0000520 membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. http://purl.obolibrary.org/obo/PLANA_0000525 organelle http://purl.obolibrary.org/obo/GO_0005575 cellular_component Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. http://purl.obolibrary.org/obo/PLANA_0000526 membrane-bounded organelle http://purl.obolibrary.org/obo/PLANA_0000525 organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. http://purl.obolibrary.org/obo/PLANA_0000527 intracellular membrane-bounded organelle http://purl.obolibrary.org/obo/PLANA_0000526 membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. http://purl.obolibrary.org/obo/PLANA_0000528 Golgi apparatus http://purl.obolibrary.org/obo/PLANA_0000527 intracellular membrane-bounded organelle A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. http://purl.obolibrary.org/obo/PLANA_0000529 nucleus http://purl.obolibrary.org/obo/PLANA_0000527 intracellular membrane-bounded organelle A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. http://purl.obolibrary.org/obo/PLANA_0000530 secretory vesicle http://purl.obolibrary.org/obo/PLANA_0000527 intracellular membrane-bounded organelle A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. http://purl.obolibrary.org/obo/PLANA_0000531 non-membrane-bounded organelle http://purl.obolibrary.org/obo/PLANA_0000525 organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. http://purl.obolibrary.org/obo/PLANA_0000532 nuclear part http://purl.obolibrary.org/obo/PLANA_0000509 intracellular part Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. http://purl.obolibrary.org/obo/PLANA_0000533 nucleolus http://purl.obolibrary.org/obo/PLANA_0000532 nuclear part A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. http://purl.obolibrary.org/obo/PLANA_0000534 chromatin http://purl.obolibrary.org/obo/PLANA_0000532 nuclear part The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome. http://purl.obolibrary.org/obo/PLANA_0000535 heterochromatin http://purl.obolibrary.org/obo/PLANA_0000534 chromatin A compact and highly condensed form of chromatin. http://purl.obolibrary.org/obo/PLANA_0000536 euchromatin http://purl.obolibrary.org/obo/PLANA_0000534 chromatin A dispersed and relatively uncompacted form of chromatin. http://purl.obolibrary.org/obo/PLANA_0000537 ribosome http://purl.obolibrary.org/obo/PLANA_0000519 intracellular non-membrane-bounded organelle An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ https://www.worldcat.org/search?q=bn%3A0198506732 ] http://purl.obolibrary.org/obo/PLANA_0000538 axon tract http://purl.obolibrary.org/obo/PLANA_0000113 tissue A group of axons linking two or more neuropils and having a common origin, termination http://purl.obolibrary.org/obo/PLANA_0000539 electrically responsive cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell A cell whose function is determined by its response to an electric signal. http://purl.obolibrary.org/obo/PLANA_0000540 electrically signaling cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell A cell that initiates an electrical signal and passes that signal to another cell. http://purl.obolibrary.org/obo/PLANA_0000541 nerve http://purl.obolibrary.org/obo/PLANA_0000113 tissue An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. http://purl.obolibrary.org/obo/PLANA_0000543 neuron projection bundle http://purl.obolibrary.org/obo/PLANA_0000538 axon tract A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. http://purl.obolibrary.org/obo/PLANA_0000545 afferent neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron A neuron which conveys sensory information centrally from the periphery. http://purl.obolibrary.org/obo/PLANA_0000546 bipolar neuron http://purl.obolibrary.org/obo/PLANA_0000550 interneuron A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. http://purl.obolibrary.org/obo/PLANA_0000547 commissural neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron A neuron that has an axon which crosses the midline. http://purl.obolibrary.org/obo/PLANA_0000548 efferent neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron A neuron which sends impulses peripherally to activate muscles or secretory cells. http://purl.obolibrary.org/obo/PLANA_0000549 excitatory motor neuron http://purl.obolibrary.org/obo/PLANA_0000564 peripheral nervous system neuron A motor neuron that is capable of directly inducing muscle contraction. http://purl.obolibrary.org/obo/PLANA_0000550 interneuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. http://purl.obolibrary.org/obo/PLANA_0000552 sensory neuron http://purl.obolibrary.org/obo/PLANA_0000545 afferent neuron Any neuron having a sensory function; an afferent neuron conveying sensory impulses. http://purl.obolibrary.org/obo/PLANA_0000553 motor neuron http://purl.obolibrary.org/obo/PLANA_0000548 efferent neuron An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. http://purl.obolibrary.org/obo/PLANA_0000556 neurosecretory neuron http://purl.obolibrary.org/obo/PLANA_0000105 secretory cell Neuronal cells which synthesize, store and release neurohormones. http://purl.obolibrary.org/obo/PLANA_0000558 sympathetic neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides. http://purl.obolibrary.org/obo/PLANA_0000559 unipolar neuron http://purl.obolibrary.org/obo/PLANA_0000552 sensory neuron Neuron with one neurite that extends from the cell body. http://purl.obolibrary.org/obo/PLANA_0000560 multipolar neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron Neuron with an axon and two or more dendrites. http://purl.obolibrary.org/obo/PLANA_0000561 neuron associated cell (sensu Nematoda and Protostomia) http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell Cells that are in close proximity to neurons. http://purl.obolibrary.org/obo/PLANA_0000562 central nervous system neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron Any neuron that is part of a central nervous system. http://purl.obolibrary.org/obo/PLANA_0000564 peripheral nervous system neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron Any neuron that is part of a peripheral nervous system. http://purl.obolibrary.org/obo/PLANA_0000565 autonomic neuron http://purl.obolibrary.org/obo/PLANA_0000564 peripheral nervous system neuron A neruon whose cell body is within an autonomic ganglion. http://purl.obolibrary.org/obo/PLANA_0000566 enteric neuron http://purl.obolibrary.org/obo/PLANA_0000565 autonomic neuron A neruon contained within with the enteric nervous system (gastrodermal plexus). http://purl.obolibrary.org/obo/PLANA_0001005 basal lamina of epidermis http://purl.obolibrary.org/obo/UBERON_0000476 acellular anatomical structure Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue. http://purl.obolibrary.org/obo/PLANA_0004503 adult hermaphrodite http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage A fully formed, sexually mature organism that reproduces through cross-fertilization. http://purl.obolibrary.org/obo/PLANA_0004504 asexual adult http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage Asexually reproducing Schmidtea mediterranea exist as constitutive adults, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system. http://purl.obolibrary.org/obo/PLANA_0004506 testis somatic gonadal cell http://purl.obolibrary.org/obo/PLANA_0002096 somatic gonadal cell dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation. http://purl.obolibrary.org/obo/PLANA_0004507 ovarian somatic gonadal cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia. http://purl.obolibrary.org/obo/PLANA_0007503 sagittal plane of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Anatomical plane which divides the body into right and left parts. This plane passes through the midline at the midline but does not always the midline. http://purl.obolibrary.org/obo/PLANA_0007509 plasma membrane http://purl.obolibrary.org/obo/PLANA_0000520 membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. http://purl.obolibrary.org/obo/PLANA_0007511 extracellular organelle http://purl.obolibrary.org/obo/PLANA_0000525 organelle Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. http://purl.obolibrary.org/obo/PLANA_0007512 mitochondrion http://purl.obolibrary.org/obo/PLANA_0000527 intracellular membrane-bounded organelle A spherical to rod shaped organelle that generates the majority of a cell's supply of ATP via cellular respiration. Mitochondria have their own genome and consist of outer and inner membranes, the latter folds inward to form cristae. This folding increases the surface area of the membrane and thus increases the space available to produce ATP. The inner and outer membranes are separated by an intermembrane space, and the inner membrane encloses the matrix. http://purl.obolibrary.org/obo/PLANA_0007513 endoplasmic reticulum http://purl.obolibrary.org/obo/PLANA_0000527 intracellular membrane-bounded organelle Network of interconnected, flattened, and/or tubular membrane, known as cisternae. This membrane is contiguous with the outer nuclear membrane. The endoplasmic reticulum is involved in both protein and lipid synthesis. http://purl.obolibrary.org/obo/PLANA_0007514 rough endoplasmic reticulum http://purl.obolibrary.org/obo/PLANA_0007513 endoplasmic reticulum Network of interconnected, flattened, and/or tubular membrane, known as cisternae. This membrane is contiguous with the outer nuclear membrane. The endoplasmic reticulum is involved in both protein and lipid synthesis. The outer surface is studded with protein-synthesizing particles known as ribosomes. http://purl.obolibrary.org/obo/PLANA_0007515 smooth endoplasmic reticulum http://purl.obolibrary.org/obo/PLANA_0007513 endoplasmic reticulum Endoplamic reticulum that does not contain ribosomes, which synthesizes lipids, phospholipids, and steroids. http://purl.obolibrary.org/obo/PLANA_0007516 nuclear pore http://purl.obolibrary.org/obo/PLANA_0002079 pore Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. http://purl.obolibrary.org/obo/PLANA_0007518 lysosome http://purl.obolibrary.org/obo/PLANA_0000527 intracellular membrane-bounded organelle The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers. http://purl.obolibrary.org/obo/PLANA_0007519 anterior-posterior axis of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Axis that runs along the long axis of the animal from anterior (head) to posterior (tail). It is perpendicular to the dorsoventral axis and as such, it splits dorsal and ventral regions of the animal to either side. http://purl.obolibrary.org/obo/PLANA_0007520 dorsal-ventral axis of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Axis that runs along the short axis of the animal, perpendicular to the anteroposterior axis, running from the dorsal (back) side of the animal to the ventral (belly) side of the animal. This axis splits anterior and posterior regions of the animal to either side. http://purl.obolibrary.org/obo/PLANA_0007521 left-right axis of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Axis perpendicular to both the anteroposterior and dorsoventral axis that runs from the left side of the animal, through the medial region (center) and out to the right side. http://purl.obolibrary.org/obo/PLANA_0007522 medial-lateral axis of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Axis that runs from the center of the body, starting at the anteroposterior axis and out to the lateral (left, right, dorsal or ventral) surface of the animal. http://purl.obolibrary.org/obo/PLANA_0007523 proximal-distal axis of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Axis that starts at the distal part of an appendage, closest to the body, and runs to the proximal part of an appendage, farthest from the body. http://purl.obolibrary.org/obo/PLANA_0007524 anterior pole http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD. http://purl.obolibrary.org/obo/PLANA_0007525 posterior pole http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region Distinct posterior cluster of muscle cells located at the midline which express wnt1. http://purl.obolibrary.org/obo/PLANA_0007528 glial cell http://purl.obolibrary.org/obo/BFO_0000040 material entity A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. http://purl.obolibrary.org/obo/PLANA_0007529 ganglion http://purl.obolibrary.org/obo/PLANA_0000113 tissue A biological tissue mass of nerve cell bodies. http://purl.obolibrary.org/obo/PLANA_0007534 pharynx inner epithelium http://purl.obolibrary.org/obo/PLANA_0002023 ciliated epithelium Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft. http://purl.obolibrary.org/obo/PLANA_0007535 pharynx circular muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell Pharynx muscle fibers running circumferentially about the pharynx. http://purl.obolibrary.org/obo/PATO_0000001 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities http://purl.obolibrary.org/obo/PATO_0000051 morphology http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. http://purl.obolibrary.org/obo/PATO_0000052 shape http://purl.obolibrary.org/obo/PATO_0000051 morphology A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). http://purl.obolibrary.org/obo/PATO_0000133 orientation http://purl.obolibrary.org/obo/PATO_0000140 position A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object. http://purl.obolibrary.org/obo/PATO_0000140 position http://purl.obolibrary.org/obo/PATO_0001018 physical quality A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. http://purl.obolibrary.org/obo/PATO_0001018 physical quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. http://purl.obolibrary.org/obo/PATO_0001241 physical object quality http://purl.obolibrary.org/obo/PATO_0000001 quality A quality which inheres in a continuant. http://purl.obolibrary.org/obo/PATO_0001875 triangular http://purl.obolibrary.org/obo/PATO_0002006 2-D shape A shape quality inhering in a bearer by virtue of the bearer's having three angles. http://purl.obolibrary.org/obo/PATO_0001955 cuneate http://purl.obolibrary.org/obo/PATO_0001875 triangular A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base. http://purl.obolibrary.org/obo/PATO_0002006 2-D shape http://purl.obolibrary.org/obo/PATO_0000052 shape A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. http://purl.obolibrary.org/obo/PATO_0005024 longitudinal orientation http://purl.obolibrary.org/obo/PATO_0000133 orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis. http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that has temporal parts and that happens, unfolds or develops through time. http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. http://purl.obolibrary.org/obo/IAO_0000028 symbol http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant A generically dependent continuant that is about some thing. http://purl.obolibrary.org/obo/IAO_0000078 curation status specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part http://purl.obolibrary.org/obo/IAO_0000027 data item Data about an ontology part is a data item about a part of an ontology, for example a term http://purl.obolibrary.org/obo/IAO_0000225 obsolescence reason specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000409 denotator type http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part A denotator type indicates how a term should be interpreted from an ontological perspective. http://purl.obolibrary.org/obo/OBI_0000011 planned process http://purl.obolibrary.org/obo/BFO_0000015 process A process that realizes a plan which is the concretization of a plan specification. http://purl.obolibrary.org/obo/GO_0140014 mitotic nuclear division http://purl.obolibrary.org/obo/GO_1903047 mitotic cell cycle process A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. http://purl.obolibrary.org/obo/PLANA_0007556 embryonic pharynx lumen http://purl.obolibrary.org/obo/PLANA_0002053 lumen A lumen enclosed by the embryonic pharynx epithelial cells through which yolk cells are transported into the embryonic gut cavity. http://purl.obolibrary.org/obo/PLANA_0007550 serotonergic neural progenitor cell http://purl.obolibrary.org/obo/PLANA_0000012 neural progenitor cell piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons. http://purl.obolibrary.org/obo/PLANA_0007543 TrpA+ central nervous system neuron http://purl.obolibrary.org/obo/BFO_0000040 material entity A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2. http://purl.obolibrary.org/obo/GO_0006996 organelle organization http://purl.obolibrary.org/obo/GO_0016043 cellular component organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0007132 meiotic metaphase I http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I. http://purl.obolibrary.org/obo/GO_0007133 meiotic anaphase I http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I. http://purl.obolibrary.org/obo/GO_0007134 meiotic telophase I http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase The cell cycle phase which follows anaphase I of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. http://purl.obolibrary.org/obo/GO_0007136 meiotic prophase II http://purl.obolibrary.org/obo/GO_0051324 prophase The cell cycle phase which is the first stage of meiosis II and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. http://purl.obolibrary.org/obo/GO_0007137 meiotic metaphase II http://purl.obolibrary.org/obo/GO_0051323 metaphase The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II. http://purl.obolibrary.org/obo/GO_0007138 meiotic anaphase II http://purl.obolibrary.org/obo/GO_0051322 anaphase The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II. http://purl.obolibrary.org/obo/GO_0007139 meiotic telophase II http://purl.obolibrary.org/obo/GO_0051326 telophase The cell cycle phase which follows anaphase II of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. http://purl.obolibrary.org/obo/GO_0016043 cellular component organization http://purl.obolibrary.org/obo/GO_0071840 cellular component organization or biogenesis A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. http://purl.obolibrary.org/obo/GO_0098765 meiosis II cell cycle phase http://purl.obolibrary.org/obo/GO_0098762 meiotic cell cycle phase A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division). http://purl.obolibrary.org/obo/GO_0051325 interphase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs. http://purl.obolibrary.org/obo/GO_0051327 meiotic M phase http://purl.obolibrary.org/obo/GO_0000279 M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a meiotic cell cycle. http://purl.obolibrary.org/obo/GO_0051330 meiotic G1 phase http://purl.obolibrary.org/obo/GO_0051318 G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis. http://purl.obolibrary.org/obo/GO_0051331 meiotic G2 phase http://purl.obolibrary.org/obo/GO_0051319 G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis. http://purl.obolibrary.org/obo/GO_0051332 meiotic S phase http://purl.obolibrary.org/obo/GO_0051320 S phase The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle. http://purl.obolibrary.org/obo/GO_0098762 meiotic cell cycle phase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase One of the distinct periods or stages into which the meiotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity http://purl.obolibrary.org/obo/UBERON_0001062 anatomical entity Anatomical entity that has mass. http://purl.obolibrary.org/obo/UBERON_0000475 organism subdivision http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. http://purl.obolibrary.org/obo/UBERON_0000476 acellular anatomical structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://purl.obolibrary.org/obo/UBERON_0002553 anatomical cavity http://purl.obolibrary.org/obo/UBERON_0001062 anatomical entity Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. http://purl.obolibrary.org/obo/UBERON_0007567 regenerating anatomical structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure An anatomical structure that is undergoing regeneration. http://purl.obolibrary.org/obo/PLANA_0000001 Stage 1 http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage A stage of Smed embryonic development, 0 - 2 days post-egg capsule deposition at 20˚C. Zygote and dispersed blastomere cleavage in a yolk syncytium. http://purl.obolibrary.org/obo/PLANA_0000002 Stage 2 http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 3 days post-egg capsule deposition at 20˚C. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall. http://purl.obolibrary.org/obo/PLANA_0000003 Stage 3 http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 4 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. http://purl.obolibrary.org/obo/PLANA_0000004 Stage 4 http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 3 - 5 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. http://purl.obolibrary.org/obo/PLANA_0000005 Stage 5 http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 5-7 days post-egg capsule deposition at 20˚C. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity. http://purl.obolibrary.org/obo/PLANA_0000006 Stage 6 http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 7 - 9 days post-egg capsule deposition at 20˚C. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. http://purl.obolibrary.org/obo/PLANA_0000007 Stage 7 http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 9 - 11 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. http://purl.obolibrary.org/obo/PLANA_0000008 Stage 8 http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 13 - 15 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Hatching. http://purl.obolibrary.org/obo/PLANA_0000009 sigma neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors. http://purl.obolibrary.org/obo/PLANA_0000011 protonephridial progenitor cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr,required for maintenance and regeneration of protonephridial cell types. http://purl.obolibrary.org/obo/PLANA_0000012 neural progenitor cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system. http://purl.obolibrary.org/obo/PLANA_0000014 zeta neoblast http://purl.obolibrary.org/obo/PLANA_0000033 epidermal progenitor cell An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). http://purl.obolibrary.org/obo/PLANA_0000016 pharynx http://purl.obolibrary.org/obo/BFO_0000040 material entity A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types. http://purl.obolibrary.org/obo/PLANA_0000017 photoreceptor neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain. http://purl.obolibrary.org/obo/PLANA_0000018 Category 4 cell http://purl.obolibrary.org/obo/PLANA_0000015 non ciliated epithelial cell Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells. http://purl.obolibrary.org/obo/PLANA_0000019 muscle progenitor cell http://purl.obolibrary.org/obo/PLANA_0000120 progenitor cell Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers. http://purl.obolibrary.org/obo/PLANA_0000020 protonephridia http://purl.obolibrary.org/obo/BFO_0000040 material entity Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. http://purl.obolibrary.org/obo/PLANA_0000022 Category 5 cell http://purl.obolibrary.org/obo/PLANA_0002032 epidermal cell Post-mitotic, ciliated epidermal cells. http://purl.obolibrary.org/obo/PLANA_0000023 embryonic pharynx http://purl.obolibrary.org/obo/PLANA_0002120 extraembryonic organ An innervated, muscular pump that ingests yolk cells into the gut cavity. The embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7. http://purl.obolibrary.org/obo/PLANA_0000025 nervous system http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. http://purl.obolibrary.org/obo/PLANA_0000026 gut http://purl.obolibrary.org/obo/BFO_0000040 material entity The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the gut through the pharynx. http://purl.obolibrary.org/obo/PLANA_0000028 Category 2 cell http://purl.obolibrary.org/obo/PLANA_0002095 somatic cell Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. http://purl.obolibrary.org/obo/PLANA_0000029 primitive ectoderm http://purl.obolibrary.org/obo/PLANA_0002120 extraembryonic organ A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7. http://purl.obolibrary.org/obo/PLANA_0000030 midline http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region The median line/ plane of bilateral symmetry along the anteroposterior axis. http://purl.obolibrary.org/obo/PLANA_0000031 pigment cup cell http://purl.obolibrary.org/obo/BFO_0000040 material entity Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. http://purl.obolibrary.org/obo/PLANA_0000032 dorsal midline http://purl.obolibrary.org/obo/BFO_0000040 material entity The median line/plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal. http://purl.obolibrary.org/obo/PLANA_0000033 epidermal progenitor cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs. http://purl.obolibrary.org/obo/PLANA_0000034 epidermis http://purl.obolibrary.org/obo/BFO_0000040 material entity A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal. http://purl.obolibrary.org/obo/PLANA_0000035 Category 3 cell http://purl.obolibrary.org/obo/PLANA_0002095 somatic cell Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells. http://purl.obolibrary.org/obo/PLANA_0000036 eye http://purl.obolibrary.org/obo/BFO_0000040 material entity An organ that detects light. http://purl.obolibrary.org/obo/PLANA_0000038 ventral midline http://purl.obolibrary.org/obo/BFO_0000040 material entity The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal. http://purl.obolibrary.org/obo/PLANA_0000039 gamma neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. http://purl.obolibrary.org/obo/PLANA_0000041 aboral hemisphere http://purl.obolibrary.org/obo/BFO_0000004 independent continuant Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx. http://purl.obolibrary.org/obo/PLANA_0000042 anterior primary gut branch http://purl.obolibrary.org/obo/PLANA_0002086 primary gut branch The single, central gut branch of the triclad gut anterior to the pharynx. http://purl.obolibrary.org/obo/PLANA_0000043 dorsal ventral margin of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Region along the edge of the animal where the dorsal and ventral surfaces meet. http://purl.obolibrary.org/obo/PLANA_0000044 cephalic ganglia http://purl.obolibrary.org/obo/BFO_0000040 material entity The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head. http://purl.obolibrary.org/obo/PLANA_0000045 circular muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. http://purl.obolibrary.org/obo/PLANA_0000046 clonogenic neoblast http://purl.obolibrary.org/obo/PLANA_0002095 somatic cell Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm. http://purl.obolibrary.org/obo/PLANA_0000047 collecting duct http://purl.obolibrary.org/obo/PLANA_0000113 tissue Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. http://purl.obolibrary.org/obo/PLANA_0000048 diagonal muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell Body wall muscle fibers arrayed diagonally along the anteroposterior axis. http://purl.obolibrary.org/obo/PLANA_0000049 digestive system http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. http://purl.obolibrary.org/obo/PLANA_0000053 distal tubule http://purl.obolibrary.org/obo/PLANA_0000113 tissue Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. http://purl.obolibrary.org/obo/PLANA_0000054 dorsal region of the epidermis http://purl.obolibrary.org/obo/BFO_0000040 material entity Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. http://purl.obolibrary.org/obo/PLANA_0000055 dorsal stripe http://purl.obolibrary.org/obo/PLANA_0002023 ciliated epithelium Ciliated epithelial cells along the dorsal midline. http://purl.obolibrary.org/obo/PLANA_0000056 ectolecithal embryo http://purl.obolibrary.org/obo/PLANA_0000116 embryo Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells. http://purl.obolibrary.org/obo/PLANA_0000058 embryonic digestive system http://purl.obolibrary.org/obo/PLANA_0000063 extraembryonic structure A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals. http://purl.obolibrary.org/obo/PLANA_0000059 embryonic gut cell http://purl.obolibrary.org/obo/PLANA_0004518 extraembryonic cell Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7. http://purl.obolibrary.org/obo/PLANA_0000060 embryonic wall http://purl.obolibrary.org/obo/BFO_0000004 independent continuant The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. http://purl.obolibrary.org/obo/PLANA_0000061 enteric musculature http://purl.obolibrary.org/obo/PLANA_0000013 visceral musculature Visceral muscle surrounding the gut. http://purl.obolibrary.org/obo/PLANA_0000062 esophagus http://purl.obolibrary.org/obo/PLANA_0000113 tissue Attachment between the triclad gut and the proximal end of the pharynx. http://purl.obolibrary.org/obo/PLANA_0000063 extraembryonic structure http://purl.obolibrary.org/obo/UBERON_0005423 developing anatomical structure A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. http://purl.obolibrary.org/obo/PLANA_0000064 flame bulb http://purl.obolibrary.org/obo/PLANA_0000113 tissue Terminal structure of protonephridia unit; consists of flame cells. http://purl.obolibrary.org/obo/PLANA_0000065 flame cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the filtration weir‚ or filtration diaphragm, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin. http://purl.obolibrary.org/obo/PLANA_0000066 gastrodermis http://purl.obolibrary.org/obo/PLANA_0002118 epithelium The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. http://purl.obolibrary.org/obo/PLANA_0000067 goblet cell http://purl.obolibrary.org/obo/PLANA_0000105 secretory cell Secretory cells that release digestive enzymes into the lumen of the intestine. http://purl.obolibrary.org/obo/PLANA_0000068 embryonic gut cavity http://purl.obolibrary.org/obo/UBERON_0002553 anatomical cavity Cavity encompassed by the embryonic digestive tract, prior to formation of the branched defintive gut. http://purl.obolibrary.org/obo/PLANA_0000069 inner longitudinal muscle cell http://purl.obolibrary.org/obo/PLANA_0000071 longitudinal muscle cell Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. http://purl.obolibrary.org/obo/PLANA_0000070 intestinal phagocyte http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell Absorptive digestive cells that engulf food particles for intracellular digestion. http://purl.obolibrary.org/obo/PLANA_0000071 longitudinal muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. http://purl.obolibrary.org/obo/PLANA_0000072 mouth http://purl.obolibrary.org/obo/BFO_0000040 material entity The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. http://purl.obolibrary.org/obo/PLANA_0000074 oocyte http://purl.obolibrary.org/obo/PLANA_0000122 gamete A female germ cell that has entered meiosis. http://purl.obolibrary.org/obo/PLANA_0000075 optic cup http://purl.obolibrary.org/obo/PLANA_0000113 tissue A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. http://purl.obolibrary.org/obo/PLANA_0000076 oral hemisphere http://purl.obolibrary.org/obo/BFO_0000004 independent continuant Stage 3-5 embryo hemisphere centered around the embryonic pharynx. http://purl.obolibrary.org/obo/PLANA_0000078 outer longitudinal muscle cell http://purl.obolibrary.org/obo/PLANA_0000071 longitudinal muscle cell Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. http://purl.obolibrary.org/obo/PLANA_0000079 parenchymal musculature http://purl.obolibrary.org/obo/BFO_0000040 material entity Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles. http://purl.obolibrary.org/obo/PLANA_0000080 peripheral nervous system http://purl.obolibrary.org/obo/PLANA_0000025 nervous system A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. http://purl.obolibrary.org/obo/PLANA_0000081 pharynx pouch http://purl.obolibrary.org/obo/PLANA_0000113 tissue An epithelial structure housing the pharynx, connected to the esophagus and mouth. http://purl.obolibrary.org/obo/PLANA_0000084 posterior primary gut branch http://purl.obolibrary.org/obo/PLANA_0002086 primary gut branch The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. http://purl.obolibrary.org/obo/PLANA_0000085 primitive gut cell http://purl.obolibrary.org/obo/PLANA_0004518 extraembryonic cell A phagocytic cell closely associated with the embryonic pharynx. http://purl.obolibrary.org/obo/PLANA_0000087 proximal tubule http://purl.obolibrary.org/obo/PLANA_0000113 tissue Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma. http://purl.obolibrary.org/obo/PLANA_0000088 renal system http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system The renal system is an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. http://purl.obolibrary.org/obo/PLANA_0000089 secondary gut branch http://purl.obolibrary.org/obo/PLANA_0002119 gut branch Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. http://purl.obolibrary.org/obo/PLANA_0000090 sperm http://purl.obolibrary.org/obo/PLANA_0000122 gamete A mature male germ cell that develops from a spermatid. http://purl.obolibrary.org/obo/PLANA_0000092 yolk syncytium http://purl.obolibrary.org/obo/PLANA_0002136 syncytium Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. http://purl.obolibrary.org/obo/PLANA_0000093 tertiary gut branch http://purl.obolibrary.org/obo/PLANA_0002119 gut branch Gut branches originating from and connected to the secondary gut branches. http://purl.obolibrary.org/obo/PLANA_0000095 trail cell http://purl.obolibrary.org/obo/PLANA_0000429 neoblast Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup. http://purl.obolibrary.org/obo/PLANA_0000096 ventral epidermis http://purl.obolibrary.org/obo/BFO_0000040 material entity Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells http://purl.obolibrary.org/obo/PLANA_0000097 ventral nerve cord http://purl.obolibrary.org/obo/BFO_0000040 material entity The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO]. http://purl.obolibrary.org/obo/PLANA_0000098 zygote http://purl.obolibrary.org/obo/PLANA_0000136 whole organism Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ]. http://purl.obolibrary.org/obo/PLANA_0000099 neuron http://purl.obolibrary.org/obo/PLANA_0000540 electrically signaling cell The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. http://purl.obolibrary.org/obo/PLANA_0000100 epithelial cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where the apical part is directed towards the lumen and the basal part to the basal lamina. http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell http://purl.obolibrary.org/obo/PLANA_0000539 electrically responsive cell A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region http://purl.obolibrary.org/obo/UBERON_0000475 organism subdivision A subdivision of an anatomical compartment. http://purl.obolibrary.org/obo/PLANA_0000103 central nervous system http://purl.obolibrary.org/obo/PLANA_0000025 nervous system The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. http://purl.obolibrary.org/obo/PLANA_0000104 rhabdite http://purl.obolibrary.org/obo/PLANA_0000430 epithelial cell component Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions. http://purl.obolibrary.org/obo/PLANA_0000105 secretory cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell A cell that specializes in controlled release of one or more substances. http://purl.obolibrary.org/obo/PLANA_0000106 ciliated epithelial cell http://purl.obolibrary.org/obo/PLANA_0000100 epithelial cell An epithelial cell that has cilia. http://purl.obolibrary.org/obo/PLANA_0000107 yolk cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. http://purl.obolibrary.org/obo/PLANA_0000110 pharynx progenitor cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the pharynx. http://purl.obolibrary.org/obo/PLANA_0000113 tissue http://purl.obolibrary.org/obo/PLANA_0000427 multicellular anatomical structure Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system http://purl.obolibrary.org/obo/PLANA_0000427 multicellular anatomical structure Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. http://purl.obolibrary.org/obo/PLANA_0000116 embryo http://purl.obolibrary.org/obo/PLANA_0000136 whole organism Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. http://purl.obolibrary.org/obo/PLANA_0000117 embryonic structure http://purl.obolibrary.org/obo/UBERON_0005423 developing anatomical structure Anatomical structure that is part of an embryo. http://purl.obolibrary.org/obo/PLANA_0000118 collecting duct epithelial cell http://purl.obolibrary.org/obo/PLANA_0000015 non ciliated epithelial cell Nonciliated epithelial cells that assemble into collecting ducts. http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell http://purl.obolibrary.org/obo/PLANA_0002095 somatic cell A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals. http://purl.obolibrary.org/obo/PLANA_0000120 progenitor cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program http://purl.obolibrary.org/obo/PLANA_0000121 stem cell http://purl.obolibrary.org/obo/PLANA_0000499 cell A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. http://purl.obolibrary.org/obo/PLANA_0000122 gamete http://purl.obolibrary.org/obo/PLANA_0000227 germ cell A mature sexual reproductive cell having a single set of unpaired chromosomes. http://purl.obolibrary.org/obo/PLANA_0000123 embryonic cell http://purl.obolibrary.org/obo/PLANA_0000499 cell A cell of the embryo. http://purl.obolibrary.org/obo/PLANA_0000124 visual system http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system The sensory system subserving the sense of vision. http://purl.obolibrary.org/obo/PLANA_0000125 sensory system http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. http://purl.obolibrary.org/obo/PLANA_0000126 reproductive system http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system Anatomical system that has as its parts the organs concerned with reproduction. http://purl.obolibrary.org/obo/PLANA_0000127 oviduct epithelial cell http://purl.obolibrary.org/obo/PLANA_0000106 ciliated epithelial cell Ciliated epithelial cells that assemble into the oviduct. http://purl.obolibrary.org/obo/PLANA_0000128 sperm duct epithelial cell http://purl.obolibrary.org/obo/PLANA_0000106 ciliated epithelial cell Ciliated epithelial cells comprising the sperm ducts. http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface http://purl.obolibrary.org/obo/CARO_0000010 anatomical boundary A 2D surface of an anatomical continuant. http://purl.obolibrary.org/obo/BSPO_0000010 anatomical axis http://purl.obolibrary.org/obo/CARO_0000008 anatomical line A straight line through space, intersecting an anatomical entity. http://purl.obolibrary.org/obo/BSPO_0000013 anterior-posterior axis http://purl.obolibrary.org/obo/BSPO_0000010 anatomical axis An axis that extends through an organism from head end to opposite end of body or tail. http://purl.obolibrary.org/obo/BSPO_0000014 apical-basal axis relative to substrate http://purl.obolibrary.org/obo/BSPO_0000010 anatomical axis An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. http://purl.obolibrary.org/obo/BSPO_0000015 proximal-distal axis http://purl.obolibrary.org/obo/BSPO_0000010 anatomical axis An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). http://purl.obolibrary.org/obo/BSPO_0000016 dorsal-ventral axis http://purl.obolibrary.org/obo/BSPO_0000010 anatomical axis An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. http://purl.obolibrary.org/obo/BSPO_0000017 left-right axis http://purl.obolibrary.org/obo/BSPO_0000010 anatomical axis An axis that bisects an organism from left to right sides of body, through a sagittal plane. http://purl.obolibrary.org/obo/BSPO_0000018 transverse plane http://purl.obolibrary.org/obo/BSPO_0000400 anatomical plane Anatomical plane that divides body into anterior and posterior parts. http://purl.obolibrary.org/obo/BSPO_0000019 horizontal plane http://purl.obolibrary.org/obo/BSPO_0000400 anatomical plane Anatomical plane that divides bilateral body into dorsal and ventral parts. http://purl.obolibrary.org/obo/BSPO_0000026 antero-dorsal region http://purl.obolibrary.org/obo/BSPO_0000079 dorsal region Anatomical region that overlaps the anterior and dorsal regions of a body or body part. http://purl.obolibrary.org/obo/BSPO_0000027 antero-ventral region http://purl.obolibrary.org/obo/BSPO_0000084 ventral region Anatomical region that overlaps the anterior and ventral regions of a body or body part. http://purl.obolibrary.org/obo/BSPO_0000028 postero-lateral region http://purl.obolibrary.org/obo/BSPO_0000082 lateral region Anatomical region that overlaps the posterior and lateral regions of the body or body part. http://purl.obolibrary.org/obo/BSPO_0000029 antero-lateral region http://purl.obolibrary.org/obo/BSPO_0000082 lateral region Anatomical region that overlaps the anterior and lateral regions of a body or body part. http://purl.obolibrary.org/obo/BSPO_0000030 postero-dorsal region http://purl.obolibrary.org/obo/BSPO_0000079 dorsal region Anatomical region that overlaps the posterior and dorsal regions of the body or body part. http://purl.obolibrary.org/obo/BSPO_0000035 postero-ventral region http://purl.obolibrary.org/obo/BSPO_0000084 ventral region Anatomical region that overlaps the posterior and ventral regions of a body or body part. http://purl.obolibrary.org/obo/BSPO_0000054 anatomical side http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region An anatomical region bounded by a plane perpendicular to an axis through the middle. http://purl.obolibrary.org/obo/BSPO_0000055 anterior side http://purl.obolibrary.org/obo/BSPO_0000054 anatomical side An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. http://purl.obolibrary.org/obo/BSPO_0000056 posterior side http://purl.obolibrary.org/obo/BSPO_0000054 anatomical side An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. http://purl.obolibrary.org/obo/BSPO_0000057 apical side http://purl.obolibrary.org/obo/BSPO_0000054 anatomical side Anatomical side that is located on the apical end of an organism or structure. http://purl.obolibrary.org/obo/BSPO_0000058 basal side http://purl.obolibrary.org/obo/BSPO_0000054 anatomical side Anatomical side that is located on the basal end of an organism or structure. http://purl.obolibrary.org/obo/BSPO_0000063 dorsal side http://purl.obolibrary.org/obo/BSPO_0000054 anatomical side An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. http://purl.obolibrary.org/obo/BSPO_0000068 ventral side http://purl.obolibrary.org/obo/BSPO_0000054 anatomical side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region http://purl.obolibrary.org/obo/CARO_0000003 anatomical structure A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. http://purl.obolibrary.org/obo/BSPO_0000071 anterior region http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region Anatomical region anteriorly located on the body or body part. http://purl.obolibrary.org/obo/BSPO_0000072 posterior region http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region Anatomical region posteriorly located on the body or body part. http://purl.obolibrary.org/obo/BSPO_0000073 apical region http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region Anatomical region located on the apical end on the body or body part. http://purl.obolibrary.org/obo/BSPO_0000074 basal region http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region Anatomical region located basally on the body or body part. http://purl.obolibrary.org/obo/BSPO_0000079 dorsal region http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region Anatomical region dorsally located on the body or body part. http://purl.obolibrary.org/obo/BSPO_0000080 dorso-lateral region http://purl.obolibrary.org/obo/BSPO_0000082 lateral region Anatomical region that overlaps the dorsal and lateral regions of a body or body part. http://purl.obolibrary.org/obo/BSPO_0000082 lateral region http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region Anatomical region laterally located on the body or body part. http://purl.obolibrary.org/obo/BSPO_0000084 ventral region http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region Anatomical region ventrally located on the body or body part. http://purl.obolibrary.org/obo/BSPO_0000085 ventro-lateral region http://purl.obolibrary.org/obo/BSPO_0000084 ventral region Anatomical region that overlaps the ventral and lateral regions of a body or body part. http://purl.obolibrary.org/obo/BSPO_0000196 medial-external axis http://purl.obolibrary.org/obo/BSPO_0000010 anatomical axis An anatomical axis that extends from the center of the body outwards or externally. http://purl.obolibrary.org/obo/BSPO_0000198 oral-aboral axis http://purl.obolibrary.org/obo/BSPO_0000010 anatomical axis An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. http://purl.obolibrary.org/obo/BSPO_0000371 anterior surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface Anatomical surface that is located on the anterior side of the body or body part. http://purl.obolibrary.org/obo/BSPO_0000372 posterior surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface Anatomical surface that is located on the posterior side of the body or body part. http://purl.obolibrary.org/obo/BSPO_0000373 apical surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface Anatomical surface that is located on the apical side of the body or body part. http://purl.obolibrary.org/obo/BSPO_0000374 basal surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface Anatomical surface that is located on the basal side of the body or body part. http://purl.obolibrary.org/obo/BSPO_0000379 dorsal surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface Anatomical surface that located on the dorsal side of the body or body part. http://purl.obolibrary.org/obo/BSPO_0000382 lateral surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface Anatomical surface that located on the lateral side of the body or body part. http://purl.obolibrary.org/obo/BSPO_0000384 ventral surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface Anatomical surface that is located on the ventral side of the body or body part. http://purl.obolibrary.org/obo/BSPO_0000400 anatomical plane http://purl.obolibrary.org/obo/CARO_0000010 anatomical boundary A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. http://purl.obolibrary.org/obo/BSPO_0000417 sagittal plane http://purl.obolibrary.org/obo/BSPO_0000400 anatomical plane Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. http://purl.obolibrary.org/obo/BSPO_0001001 medial-lateral axis http://purl.obolibrary.org/obo/BSPO_0000196 medial-external axis An axis that extends from the center of organism to one or other side. http://purl.obolibrary.org/obo/PLANA_0002000 adenal rhabdite http://purl.obolibrary.org/obo/PLANA_0000104 rhabdite Rhabdites that are located basally to the epidermis, in the mesenchyme. In Smed these are present in cells likely on their way to becoming part of the mature epidermis. http://purl.obolibrary.org/obo/PLANA_0002001 adherens junction http://purl.obolibrary.org/obo/PLANA_0000506 cell junction A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments. http://purl.obolibrary.org/obo/PLANA_0002002 adhesive papilla http://purl.obolibrary.org/obo/BFO_0000040 material entity Finger-like processes at the terminal pore of adhesive gland cells around the marginal adhesive zone. They protrude past the epidermis and are longer microvilli, and shorter than cilia. http://purl.obolibrary.org/obo/PLANA_0002003 amputation http://purl.obolibrary.org/obo/PLANA_0002026 cut A wound resulting in two or more separate tissue fragments. http://purl.obolibrary.org/obo/PLANA_0002004 anterior gut branch http://purl.obolibrary.org/obo/PLANA_0002119 gut branch A branch of the triclad gut located anterior to the pharynx. http://purl.obolibrary.org/obo/PLANA_0002005 anterior tip http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region The anterior-medial region of the head margin. http://purl.obolibrary.org/obo/PLANA_0002006 antrum http://purl.obolibrary.org/obo/UBERON_0002553 anatomical cavity A chamber formation in an organ. http://purl.obolibrary.org/obo/PLANA_0002007 auricle http://purl.obolibrary.org/obo/BFO_0000040 material entity A sense organ located along the dorsolateral head margin. The auricular groove is highly innervtated by ciliated sensory neurons, and has an altered epidermis devoid of rhabdites and gland cells. http://purl.obolibrary.org/obo/PLANA_0002008 axon http://purl.obolibrary.org/obo/PLANA_0000501 cell projection The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. http://purl.obolibrary.org/obo/PLANA_0002009 axoneme http://purl.obolibrary.org/obo/BFO_0000004 independent continuant The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. http://purl.obolibrary.org/obo/PLANA_0002010 basal body http://purl.obolibrary.org/obo/BFO_0000004 independent continuant A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. http://purl.obolibrary.org/obo/PLANA_0002011 brain visual center http://purl.obolibrary.org/obo/PLANA_0000113 tissue Region of the cephalic ganglia innervated by the optic nerve (posterior-projecting photoreceptor neuron fasiculated axons). http://purl.obolibrary.org/obo/PLANA_0002012 bulbar cavity http://purl.obolibrary.org/obo/UBERON_0002553 anatomical cavity An enlarged portion of the seminal vesicle, comprised of secretory epithelial cells, that connects to the ejaculatory duct within the penis papilla. http://purl.obolibrary.org/obo/PLANA_0002013 Category 1 cell http://purl.obolibrary.org/obo/PLANA_0003116 parenchymal cell Irradiation-sensitive, mesenchymal cells that are absent from the head region anterior to the eyes and the pharynx. The Category 1 designation encompasses the neoblast population. http://purl.obolibrary.org/obo/PLANA_0002014 cell body http://purl.obolibrary.org/obo/GO_0005575 cellular_component The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. http://purl.obolibrary.org/obo/PLANA_0002015 cephalic ganglia lobe http://purl.obolibrary.org/obo/PLANA_0000113 tissue One of two bilaterally symmetric structures comprising the planarian brain. http://purl.obolibrary.org/obo/PLANA_0002016 cephalic ganglia neuron http://purl.obolibrary.org/obo/BFO_0000040 material entity A central nervous system neuron located within the planarian brain. http://purl.obolibrary.org/obo/PLANA_0002017 chemical amputation http://purl.obolibrary.org/obo/PLANA_0002108 wound Amputation carried out by application of chemicals. http://purl.obolibrary.org/obo/PLANA_0002018 chemical pharynx amputation http://purl.obolibrary.org/obo/PLANA_0002017 chemical amputation Amputation of the phaynx, including the esophagus, by treatment with Sodium Azide. http://purl.obolibrary.org/obo/PLANA_0002019 chemosensory neuron http://purl.obolibrary.org/obo/PLANA_0000552 sensory neuron Any neuron that capable of some detection of chemical stimulus involved in sensory perception. http://purl.obolibrary.org/obo/PLANA_0002020 chromatoid body http://purl.obolibrary.org/obo/PLANA_0000531 non-membrane-bounded organelle A membrane-less, cytoplasmic ribonucleoprotein granule present in neoblasts and germ cells implicated in post-transcriptional regulation. The RNA helicase DHH1/RCK, Tudor, SmB, methylated substrates of PRMT5, PIWI-3 and Germinal Histone H4 localize to chromatoid bodies in neoblasts. http://purl.obolibrary.org/obo/PLANA_0002021 chromosome http://purl.obolibrary.org/obo/PLANA_0000532 nuclear part A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. http://purl.obolibrary.org/obo/PLANA_0002022 chromosome arm http://purl.obolibrary.org/obo/PLANA_0002121 chromosome part Under the microscope chromosomes appear as thin, thread-like structures. They all have a short arm and long arm separated by a primary constriction called the centromere. The short arm is designated as p and the long arm as q. http://purl.obolibrary.org/obo/PLANA_0002023 ciliated epithelium http://purl.obolibrary.org/obo/PLANA_0002118 epithelium Epithelium bearing vibratile cilia on the free surface. http://purl.obolibrary.org/obo/PLANA_0002024 cilium http://purl.obolibrary.org/obo/PLANA_0000501 cell projection A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. The longitudinal array of microtubules are almost always in a 9+2 array with 2 microtubles in the central cilia bundle and 9 sets of doublet microtubules around the perimeter. The exception to this arrangement is spermatazoa flagella, which have a 9+1 array in planarians. http://purl.obolibrary.org/obo/PLANA_0002025 commissure http://purl.obolibrary.org/obo/PLANA_0000113 tissue A bundle of nerve fibers crossing from one side to the other side of the brain or spinal cord. http://purl.obolibrary.org/obo/PLANA_0002026 cut http://purl.obolibrary.org/obo/PLANA_0002099 surgical wound A wound or cleft resulted from tissue separation into parts or laid open or penetrated with a sharp edge or instrument. http://purl.obolibrary.org/obo/PLANA_0002027 dendrite http://purl.obolibrary.org/obo/PLANA_0000501 cell projection A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. http://purl.obolibrary.org/obo/PLANA_0002028 dorsal-ventral muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell A muscle cell that runs in the transverse plane that connects the dorsal and ventral sides of the animal. http://purl.obolibrary.org/obo/PLANA_0002029 early female germ cell http://purl.obolibrary.org/obo/BFO_0000040 material entity A premeiotic female germ cell (i.e., a diploid female germline stem cell or transit amplifying oogonial cell). http://purl.obolibrary.org/obo/PLANA_0002030 early male germ cell http://purl.obolibrary.org/obo/BFO_0000040 material entity A premeiotic male germ cell (i.e., a spermatogonial stem cell or transit amplifying spermatogonial cell). http://purl.obolibrary.org/obo/PLANA_0002031 embryonic gut http://purl.obolibrary.org/obo/PLANA_0002120 extraembryonic organ A cryptic digestive cavity comprised of phagocytic embryonic gut cells. http://purl.obolibrary.org/obo/PLANA_0002032 epidermal cell http://purl.obolibrary.org/obo/PLANA_0000100 epithelial cell An epithelial cell of the integument (the outer layer of an organism). http://purl.obolibrary.org/obo/PLANA_0002033 epidermal rhabdite http://purl.obolibrary.org/obo/PLANA_0000104 rhabdite Rhabdites located within epidermal cells. http://purl.obolibrary.org/obo/PLANA_0002034 ER membrane http://purl.obolibrary.org/obo/PLANA_0000521 bounding membrane of organelle The lipid bilayer surrounding the endoplasmic reticulum. http://purl.obolibrary.org/obo/PLANA_0002035 eumelanin http://purl.obolibrary.org/obo/GO_0005575 cellular_component The black pigment that gives non-neuronal pigment cells of the optic cup their characteristic color. http://purl.obolibrary.org/obo/PLANA_0002036 excretory cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids. http://purl.obolibrary.org/obo/PLANA_0002037 extracellular matrix http://purl.obolibrary.org/obo/UBERON_0000476 acellular anatomical structure A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. http://purl.obolibrary.org/obo/PLANA_0002038 extracellular space http://purl.obolibrary.org/obo/UBERON_0000476 acellular anatomical structure That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. http://purl.obolibrary.org/obo/PLANA_0002039 fission http://purl.obolibrary.org/obo/PLANA_0002108 wound A form of asexual reproduction resulting in self-amputation of posterior tissue, generating an anterior fragment and a fission fragment. http://purl.obolibrary.org/obo/PLANA_0002040 flagellum http://purl.obolibrary.org/obo/BFO_0000004 independent continuant Planarian undulipodia consisting of spermatazoa cell posterior protrusions. Planarian spermatozoa contain two flagella and are composed of 9 + 1 axonemal microtubule arrangements in their flagella (markedly different from the 9 + 2 structures generally observed in sperm of other animals). http://purl.obolibrary.org/obo/PLANA_0002041 gap junction http://purl.obolibrary.org/obo/PLANA_0000507 cell-cell junction A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins. http://purl.obolibrary.org/obo/PLANA_0002042 genital atrium http://purl.obolibrary.org/obo/UBERON_0002553 anatomical cavity A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the genital atrium; glands surrounding the genital atrium produce the egg capsule shell. http://purl.obolibrary.org/obo/PLANA_0002043 germ cell cyst http://purl.obolibrary.org/obo/PLANA_0002136 syncytium A clonally-related group of interconnected spermatogonial or oogonial cells, enveloped by somatic gonadal cells. http://purl.obolibrary.org/obo/PLANA_0002044 germline stem cell http://purl.obolibrary.org/obo/PLANA_0000121 stem cell Stem cell that is the precursor of gametes. http://purl.obolibrary.org/obo/PLANA_0002045 glycogen granule http://purl.obolibrary.org/obo/PLANA_0002137 intracellular granule Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface. http://purl.obolibrary.org/obo/PLANA_0002046 incision http://purl.obolibrary.org/obo/PLANA_0002026 cut A surgical cut that breaches the epidermis, made with a defined edge. http://purl.obolibrary.org/obo/PLANA_0002047 pharynx inner epidermal cell http://purl.obolibrary.org/obo/PLANA_0002032 epidermal cell Epithelial cells lining the inside of the pharynx. In Smed, distally located cells are heavily ciliated. http://purl.obolibrary.org/obo/PLANA_0002048 inner zone of gland cells http://purl.obolibrary.org/obo/PLANA_0000113 tissue Gland or secretory cells sandwiched between muscle and epidermal layers in the pharynx. http://purl.obolibrary.org/obo/PLANA_0002049 intercellular junction http://purl.obolibrary.org/obo/PLANA_0000507 cell-cell junction A cell junction that forms a connection between two or more cells in a multicellular organism. http://purl.obolibrary.org/obo/PLANA_0002050 linear amputation http://purl.obolibrary.org/obo/PLANA_0002003 amputation An amputation performed with a transverse, oblique or longitudinal cut. http://purl.obolibrary.org/obo/PLANA_0002051 linear incision http://purl.obolibrary.org/obo/PLANA_0002046 incision A breach of the epidermis and optionally down into other structures though an insult with a knife or other instrument, such that the movement includes the z direction and one or more of the x y direction. http://purl.obolibrary.org/obo/PLANA_0002052 lipid droplet http://purl.obolibrary.org/obo/PLANA_0000519 intracellular non-membrane-bounded organelle An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins. http://purl.obolibrary.org/obo/PLANA_0002053 lumen http://purl.obolibrary.org/obo/UBERON_0002553 anatomical cavity The cavity or channel within a tube or tubular organ such as a blood vessel or the intestine. http://purl.obolibrary.org/obo/PLANA_0002054 marginal adhesive zone http://purl.obolibrary.org/obo/BSPO_0000086 anatomical compartment Zone present along the lateral dorsoventral boundary that sits just underneath the animal, in contact with substrates. It is comprised of bunches of adhesion gland cells whose terminal pores form pore rosettes through the dorsal ventral boundary epidermis.This region of is devoid of rhabdites. http://purl.obolibrary.org/obo/PLANA_0002055 mechanosensory neuron http://purl.obolibrary.org/obo/PLANA_0000552 sensory neuron Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception. http://purl.obolibrary.org/obo/PLANA_0002056 medial muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell Subset of dorsal-ventral muscle cells located in the medial body region. http://purl.obolibrary.org/obo/PLANA_0002057 meiotic germ cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant A germ cell undergoing meiosis. http://purl.obolibrary.org/obo/PLANA_0002058 melanosome http://purl.obolibrary.org/obo/BFO_0000040 material entity A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. http://purl.obolibrary.org/obo/PLANA_0002059 mucus http://purl.obolibrary.org/obo/UBERON_0000476 acellular anatomical structure A secreted, mucin-rich extracellular substance coating the epidermal surface of the animal implicated in gliding locomotion, substrate adhesion, innate immunity and predator avoidance. http://purl.obolibrary.org/obo/PLANA_0002060 nephridiopore http://purl.obolibrary.org/obo/PLANA_0002079 pore The external opening and terminus of a protonephridium made by a terminal cell. http://purl.obolibrary.org/obo/PLANA_0002061 neurite http://purl.obolibrary.org/obo/PLANA_0000501 cell projection Cell appendage of the neuron which includes the axon and the dendrite. http://purl.obolibrary.org/obo/PLANA_0002062 neuropeptidergic neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron A neuron that produces and releases neuropeptides at chemical synapses. http://purl.obolibrary.org/obo/PLANA_0002063 non-ciliated epidermis http://purl.obolibrary.org/obo/PLANA_0000034 epidermis Differentiating, immature epidermal cells lacking cilia. http://purl.obolibrary.org/obo/PLANA_0002064 nuclear envelope http://purl.obolibrary.org/obo/PLANA_0000520 membrane The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). http://purl.obolibrary.org/obo/PLANA_0002065 nuclear inner membrane http://purl.obolibrary.org/obo/PLANA_0000522 membrane part The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope. http://purl.obolibrary.org/obo/PLANA_0002066 nuclear lumen http://purl.obolibrary.org/obo/PLANA_0000532 nuclear part The volume enclosed by the nuclear inner membrane. http://purl.obolibrary.org/obo/PLANA_0002067 nuclear outer membrane http://purl.obolibrary.org/obo/PLANA_0000522 membrane part The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes. http://purl.obolibrary.org/obo/PLANA_0002068 nuclear periphery http://purl.obolibrary.org/obo/PLANA_0000532 nuclear part The portion of the nuclear lumen proximal to the inner nuclear membrane. http://purl.obolibrary.org/obo/PLANA_0002069 ommochrome pigment cell http://purl.obolibrary.org/obo/PLANA_0002075 pigment cell Parenchymal cells that synthesize and contain brown ommonchrome pigment. http://purl.obolibrary.org/obo/PLANA_0002070 optic nerve http://purl.obolibrary.org/obo/BFO_0000040 material entity A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila. http://purl.obolibrary.org/obo/PLANA_0002071 pharynx outer epidermal cell http://purl.obolibrary.org/obo/PLANA_0002032 epidermal cell Heavily ciliated, insunk epithelial cells bounding the outside of the pharynx. Outer pharynx epithelial cell nuclei are positioned beneath the pharynx musculature. http://purl.obolibrary.org/obo/PLANA_0002073 phagocytic cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell A cell that engulfs large particles or cells via invagination of the plasma membrane and creation of a phagosome. http://purl.obolibrary.org/obo/PLANA_0002074 pharynx tip http://purl.obolibrary.org/obo/PLANA_0000113 tissue The distal-most end of the pharnyx containing an opening to the pharynx lumen. http://purl.obolibrary.org/obo/PLANA_0002075 pigment cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell A pigment cell is a cell that contains pigment granules. http://purl.obolibrary.org/obo/PLANA_0002076 pigment granule http://purl.obolibrary.org/obo/PLANA_0000526 membrane-bounded organelle A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. http://purl.obolibrary.org/obo/PLANA_0002077 plug amputation http://purl.obolibrary.org/obo/PLANA_0002003 amputation A wound resulting from an amputation of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. http://purl.obolibrary.org/obo/PLANA_0002078 point incision http://purl.obolibrary.org/obo/PLANA_0002046 incision A breach of the epidermis made with a sharp pointed object, like a needle or an insect pin. http://purl.obolibrary.org/obo/PLANA_0002079 pore http://purl.obolibrary.org/obo/UBERON_0002553 anatomical cavity An anatomical space that is an opening, usually at the end of a canal or duct, on the surface of the integument or the lining of an internal anatomical space. http://purl.obolibrary.org/obo/PLANA_0002080 post-meiotic germ cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant A haploid gamete undergoing terminal differentiation. http://purl.obolibrary.org/obo/PLANA_0002081 postsynaptic cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane. http://purl.obolibrary.org/obo/PLANA_0002082 premeiotic germ cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant A diploid germline stem cell or transit amplifying germ cell that has not committed to undergoing meiotic DNA replication, reductive divisions or terminal differentiation. http://purl.obolibrary.org/obo/PLANA_0002083 presynaptic cell http://purl.obolibrary.org/obo/PLANA_0000099 neuron The part of a synapse that is part of the presynaptic cell. http://purl.obolibrary.org/obo/PLANA_0002084 presynaptic terminal http://purl.obolibrary.org/obo/GO_0005575 cellular_component Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it. http://purl.obolibrary.org/obo/PLANA_0002085 presynaptic vesicle http://purl.obolibrary.org/obo/PLANA_0000526 membrane-bounded organelle A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane. http://purl.obolibrary.org/obo/PLANA_0002086 primary gut branch http://purl.obolibrary.org/obo/PLANA_0002119 gut branch The largest branch of the triclad intestine. It is comprised of the gastrodermis, a columnar epithelium, surrounded by basal lamina and visceral musculature. http://purl.obolibrary.org/obo/PLANA_0002087 primitive gut http://purl.obolibrary.org/obo/PLANA_0002120 extraembryonic organ Four large phagocytic cells associated with the embryonic pharynx. http://purl.obolibrary.org/obo/PLANA_0002088 quarternary gut branch http://purl.obolibrary.org/obo/PLANA_0002119 gut branch Gut branches originating from and connected to the tertiary gut branches. http://purl.obolibrary.org/obo/PLANA_0002089 reproductive organ http://purl.obolibrary.org/obo/BFO_0000004 independent continuant An organ involved in reproduction http://purl.obolibrary.org/obo/PLANA_0002090 reproductive structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure Any anatomical structure that is part of the reproductive system. http://purl.obolibrary.org/obo/PLANA_0002091 rhabdome http://purl.obolibrary.org/obo/PLANA_0000113 tissue The light sensing structure consisting of photoreceptor neuron dendrites that project into the optic lumen and show close associations with eumelanin-containing pigment cup cells. http://purl.obolibrary.org/obo/PLANA_0002092 rhabdomere http://purl.obolibrary.org/obo/BFO_0000040 material entity The dendritic process of a bipolar photoreceptor neuron that projects into the optic cup lumen and senses light. http://purl.obolibrary.org/obo/PLANA_0002093 secretory duct http://purl.obolibrary.org/obo/PLANA_0000113 tissue A tubular structure that transports secreted or excreted substances. http://purl.obolibrary.org/obo/PLANA_0002094 secretory granule http://purl.obolibrary.org/obo/PLANA_0000526 membrane-bounded organelle A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. http://purl.obolibrary.org/obo/PLANA_0002095 somatic cell http://purl.obolibrary.org/obo/PLANA_0000499 cell One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells. http://purl.obolibrary.org/obo/PLANA_0002096 somatic gonadal cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell A non-germline cell within the ovary or testis. http://purl.obolibrary.org/obo/PLANA_0002097 specialized neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast A presumptive progenitor cell that expresses both pan-neoblast markers and pro-differentiation gene(s), frequently developmental transcription factors, implicated in lineage commitment and tissue-specific differentiation programs. http://purl.obolibrary.org/obo/PLANA_0002098 stalk http://purl.obolibrary.org/obo/UBERON_0000476 acellular anatomical structure A thin, flexible rod that anchors an egg capsule to a solid substrate. http://purl.obolibrary.org/obo/PLANA_0002099 surgical wound http://purl.obolibrary.org/obo/PLANA_0002108 wound A wound produced by non-autonomous physical means. http://purl.obolibrary.org/obo/PLANA_0002100 synapse http://purl.obolibrary.org/obo/PLANA_0000507 cell-cell junction The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. http://purl.obolibrary.org/obo/PLANA_0002101 synaptic cleft http://purl.obolibrary.org/obo/PLANA_0002038 extracellular space The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released. http://purl.obolibrary.org/obo/PLANA_0002102 synaptic vesicle http://purl.obolibrary.org/obo/PLANA_0000526 membrane-bounded organelle Vesicles that store various neurotransmitters that are released at the synapse. The release is regulated by a voltage-dependent calcium channel. Vesicles are essential for propagating nerve impulses between neurons and are constantly recreated by the cell. [Wikipedia] http://purl.obolibrary.org/obo/PLANA_0002103 synaptonemal complex http://purl.obolibrary.org/obo/PLANA_0002123 chromosomal_structural_element A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element. http://purl.obolibrary.org/obo/PLANA_0002104 tail tip http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region The posterior-medial region of the tail margin. http://purl.obolibrary.org/obo/PLANA_0002105 telomere http://purl.obolibrary.org/obo/PLANA_0002121 chromosome part The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. http://purl.obolibrary.org/obo/PLANA_0002106 septate junction http://purl.obolibrary.org/obo/PLANA_0000507 cell-cell junction A cell-cell junction in invertebrates that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other. http://purl.obolibrary.org/obo/PLANA_0002107 wedge amputation http://purl.obolibrary.org/obo/PLANA_0002003 amputation A wound resulting from a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. http://purl.obolibrary.org/obo/PLANA_0002108 wound http://purl.obolibrary.org/obo/PLANA_0002122 perturbation An injury that breaches the epidermis. http://purl.obolibrary.org/obo/PLANA_0002109 X1 cell http://purl.obolibrary.org/obo/PLANA_0002138 FACS sorted cell population A sorted cell population enriched for irradiation-sensitive, cycling cells (4n cells, with high levels of Hoescht 33342 staining) with scant cytoplasm (low levels of calcein-AM staining). X1 cells are enriched for cycling neoblasts. http://purl.obolibrary.org/obo/PLANA_0002110 X1(FS) cell http://purl.obolibrary.org/obo/PLANA_0002138 FACS sorted cell population A heterogeneous sorted cell population of unstained planarian cells with similar size and complexity to irradiation-sensitive, cycling cells contained in the X1 gate. Unlike X1 cells, X1(FS) cells are amenable to cell transplantation. http://purl.obolibrary.org/obo/PLANA_0002111 X2 cell http://purl.obolibrary.org/obo/PLANA_0002138 FACS sorted cell population A sorted cell population containing irradiation-sensitive and irradiation-insensitive cells, characterized by weak Hoescht 33342 and calcein-AM staining. X2 cell populations contain neoblasts as well as a variety of lineage-dedicated post-mitotic progenitor cells. http://purl.obolibrary.org/obo/PLANA_0002112 Xins cell http://purl.obolibrary.org/obo/PLANA_0002138 FACS sorted cell population A sorted cell population of irradiation-insensitive cells that contains a variety of post-mitotic, differentiated cell types. http://purl.obolibrary.org/obo/PLANA_0002113 postpharyngeal region http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region Posterior to the pharynx. http://purl.obolibrary.org/obo/PLANA_0002114 post-blastema region http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region Adjacent to blastema, or proximal to blastema. http://purl.obolibrary.org/obo/PLANA_0002116 fission fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment derived from a spontaneous or induced fission event. http://purl.obolibrary.org/obo/PLANA_0002118 epithelium http://purl.obolibrary.org/obo/PLANA_0000113 tissue The avascular cellular layers that cover body surfaces and cavities and may form glands. http://purl.obolibrary.org/obo/PLANA_0002119 gut branch http://purl.obolibrary.org/obo/PLANA_0000113 tissue The triclad planarian gut is serially bifrucated into connected lumens where each bifrucation is a branch. http://purl.obolibrary.org/obo/PLANA_0002120 extraembryonic organ http://purl.obolibrary.org/obo/PLANA_0000431 organ Organ that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. http://purl.obolibrary.org/obo/PLANA_0002121 chromosome part http://purl.obolibrary.org/obo/PLANA_0000532 nuclear part This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. http://purl.obolibrary.org/obo/PLANA_0002123 chromosomal_structural_element http://purl.obolibrary.org/obo/PLANA_0002121 chromosome part structural element of a chromosome, for example, a telomere and a centromere http://purl.obolibrary.org/obo/PLANA_0002125 thick fragment http://purl.obolibrary.org/obo/PLANA_0003608 longitudinal fragment A longitudinal fragment containing the preexisting midline and medial structures. http://purl.obolibrary.org/obo/PLANA_0002126 thin fragment http://purl.obolibrary.org/obo/PLANA_0003608 longitudinal fragment A longitudinal fragment lacking a midline and medial structures. http://purl.obolibrary.org/obo/PLANA_0002128 fragment http://purl.obolibrary.org/obo/UBERON_0007567 regenerating anatomical structure A piece of tissue isolated from the body. http://purl.obolibrary.org/obo/PLANA_0002129 longitudinal region http://purl.obolibrary.org/obo/BSPO_0000070 anatomical region A region bounded by any sagittal plane though the animal and the left or right side of the animal. NOTE: sagittal plane is an anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size http://purl.obolibrary.org/obo/PLANA_0002130 chemical wound http://purl.obolibrary.org/obo/PLANA_0002108 wound An intentional wound produced by non-autonomous chemical means. http://purl.obolibrary.org/obo/PLANA_0002131 plug wound http://purl.obolibrary.org/obo/PLANA_0002108 wound A wound resulting from the removal of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. http://purl.obolibrary.org/obo/PLANA_0002132 wedge wound http://purl.obolibrary.org/obo/PLANA_0002108 wound A wound resulting from the removal of a piece of tissue from the lateral margin at any given point that extends interiorly to more medial structures. http://purl.obolibrary.org/obo/PLANA_0002133 regenerating fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment that has undergone wound healing and is undergoing tissue replacement and morphallaxis. http://purl.obolibrary.org/obo/PLANA_0002134 sagittal orientation http://purl.obolibrary.org/obo/PATO_0005024 longitudinal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the sagittal plane. This plane runs longitudinally and is not necessarily medial. http://purl.obolibrary.org/obo/PLANA_0002135 parasagittal orientation http://purl.obolibrary.org/obo/PLANA_0002134 sagittal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the parasagittal plane, which runs longitudinally, and is never medial. http://purl.obolibrary.org/obo/PLANA_0002136 syncytium http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure An anatomical entity consisting of a single or a few multinucleated structures http://purl.obolibrary.org/obo/PLANA_0002137 intracellular granule http://purl.obolibrary.org/obo/PLANA_0000519 intracellular non-membrane-bounded organelle Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy. http://purl.obolibrary.org/obo/PLANA_0002138 FACS sorted cell population http://purl.obolibrary.org/obo/PLANA_0002139 derived cell population Any number of cells from dissociated planarian tissue sorted via a FACS sorter for any parameter. http://purl.obolibrary.org/obo/PLANA_0002139 derived cell population http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Cells isolated from dissociated planarian tissue. http://purl.obolibrary.org/obo/PLANA_0002140 pharynx pouch epithelium http://purl.obolibrary.org/obo/PLANA_0002118 epithelium An epithelial monolayer lining the pharynx pouch cavity. http://purl.obolibrary.org/obo/PLANA_0002141 sperm duct epithelial surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface Epithelial surface lining the sperm duct. http://purl.obolibrary.org/obo/PLANA_0002142 parenchyma http://purl.obolibrary.org/obo/PLANA_0000113 tissue A loosely organized collection of connective tissue and cells, including neoblasts and their immediate progeny, located in the space outside of the organs between the body wall musculature and the gut. http://purl.obolibrary.org/obo/PLANA_0003100 testis cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant cell which is part of the testis http://purl.obolibrary.org/obo/PLANA_0003103 eye cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant cell which is part of the eye http://purl.obolibrary.org/obo/PLANA_0003104 enteric muscle cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant cell which is part of the enteric musculature http://purl.obolibrary.org/obo/PLANA_0003108 gastrodermal cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant cell which is part of the gastrodermis http://purl.obolibrary.org/obo/PLANA_0003110 pharynx neuron http://purl.obolibrary.org/obo/BFO_0000004 independent continuant neuron which is part of the pharynx http://purl.obolibrary.org/obo/PLANA_0003111 pharynx epithelial cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant epithelial cell which is part of the pharynx http://purl.obolibrary.org/obo/PLANA_0003112 pharynx muscle cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant muscle cell which is part of the pharynx http://purl.obolibrary.org/obo/PLANA_0003113 pharynx pouch epithelial cell http://purl.obolibrary.org/obo/BFO_0000004 independent continuant epithelial cell which is part of the pharynx pouch http://purl.obolibrary.org/obo/PLANA_0003114 melanin pigment granule http://purl.obolibrary.org/obo/BFO_0000004 independent continuant pigment granule which is part of the eumelanin http://purl.obolibrary.org/obo/PLANA_0003200 G1 phase neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast neoblast undergoing mitotic G1 phase http://purl.obolibrary.org/obo/PLANA_0003201 S phase neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast neoblast undergoing mitotic S phase http://purl.obolibrary.org/obo/PLANA_0003202 G2 phase neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast neoblast undergoing mitotic G2 phase http://purl.obolibrary.org/obo/PLANA_0003203 prophase neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast neoblast undergoing mitotic prophase http://purl.obolibrary.org/obo/PLANA_0003204 metaphase neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast neoblast undergoing mitotic metaphase http://purl.obolibrary.org/obo/PLANA_0003205 anaphase neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast neoblast undergoing mitotic anaphase http://purl.obolibrary.org/obo/PLANA_0003206 telophase neoblast http://purl.obolibrary.org/obo/PLANA_0000429 neoblast neoblast undergoing mitotic telophase http://purl.obolibrary.org/obo/PLANA_0003207 G1 phase spermatogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000219 spermatogonial stem cell spermatogonial stem cell undergoing mitotic G1 phase http://purl.obolibrary.org/obo/PLANA_0003208 S phase spermatogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000219 spermatogonial stem cell spermatogonial stem cell undergoing mitotic S phase http://purl.obolibrary.org/obo/PLANA_0003209 G2 phase spermatogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000219 spermatogonial stem cell spermatogonial stem cell undergoing mitotic G2 phase http://purl.obolibrary.org/obo/PLANA_0003210 prophase spermatogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000219 spermatogonial stem cell spermatogonial stem cell undergoing mitotic prophase http://purl.obolibrary.org/obo/PLANA_0003211 metaphase spermatogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000219 spermatogonial stem cell spermatogonial stem cell undergoing mitotic metaphase http://purl.obolibrary.org/obo/PLANA_0003212 anaphase spermatogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000219 spermatogonial stem cell spermatogonial stem cell undergoing mitotic anaphase http://purl.obolibrary.org/obo/PLANA_0003213 telophase spermatogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000219 spermatogonial stem cell spermatogonial stem cell undergoing mitotic telophase http://purl.obolibrary.org/obo/PLANA_0003214 G1 phase oogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000223 oogonial stem cell oogonial stem cell undergoing mitotic G1 phase http://purl.obolibrary.org/obo/PLANA_0003215 S phase oogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000223 oogonial stem cell oogonial stem cell undergoing mitotic S phase http://purl.obolibrary.org/obo/PLANA_0003216 G2 phase oogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000223 oogonial stem cell oogonial stem cell undergoing mitotic G2 phase http://purl.obolibrary.org/obo/PLANA_0003217 prophase oogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000223 oogonial stem cell oogonial stem cell undergoing mitotic prophase http://purl.obolibrary.org/obo/PLANA_0003218 metaphase oogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000223 oogonial stem cell oogonial stem cell undergoing mitotic metaphase http://purl.obolibrary.org/obo/PLANA_0003219 anaphase oogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000223 oogonial stem cell oogonial stem cell undergoing mitotic anaphase http://purl.obolibrary.org/obo/PLANA_0003220 telophase oogonial stem cell http://purl.obolibrary.org/obo/PLANA_0000223 oogonial stem cell oogonial stem cell undergoing mitotic telophase http://purl.obolibrary.org/obo/PLANA_0003221 G1 phase spermatogonium http://purl.obolibrary.org/obo/PLANA_0000220 spermatogonium spermatogonium undergoing mitotic G1 phase http://purl.obolibrary.org/obo/PLANA_0003222 S phase spermatogonium http://purl.obolibrary.org/obo/PLANA_0000220 spermatogonium spermatogonium undergoing mitotic S phase http://purl.obolibrary.org/obo/PLANA_0003223 G2 phase spermatogonium http://purl.obolibrary.org/obo/PLANA_0000220 spermatogonium spermatogonium undergoing mitotic G2 phase http://purl.obolibrary.org/obo/PLANA_0003224 prophase spermatogonium http://purl.obolibrary.org/obo/PLANA_0000220 spermatogonium spermatogonium undergoing mitotic prophase http://purl.obolibrary.org/obo/PLANA_0003225 metaphase spermatogonia http://purl.obolibrary.org/obo/PLANA_0000220 spermatogonium spermatogonium undergoing mitotic metaphase http://purl.obolibrary.org/obo/PLANA_0003226 anaphase spermatogonia http://purl.obolibrary.org/obo/PLANA_0000220 spermatogonium spermatogonium undergoing mitotic anaphase http://purl.obolibrary.org/obo/PLANA_0003227 telophase spermatogonium http://purl.obolibrary.org/obo/PLANA_0000220 spermatogonium spermatogonium undergoing mitotic telophase http://purl.obolibrary.org/obo/PLANA_0003228 G1 phase oogonial cell http://purl.obolibrary.org/obo/PLANA_0000239 oogonial cell oogonial cell undergoing mitotic G1 phase http://purl.obolibrary.org/obo/PLANA_0003229 S phase oogonial cell http://purl.obolibrary.org/obo/PLANA_0000239 oogonial cell oogonial cell undergoing mitotic S phase http://purl.obolibrary.org/obo/PLANA_0003230 G2 phase oogonial cell http://purl.obolibrary.org/obo/PLANA_0000239 oogonial cell oogonial cell undergoing mitotic G2 phase http://purl.obolibrary.org/obo/PLANA_0003231 prophase oogonial cell http://purl.obolibrary.org/obo/PLANA_0000239 oogonial cell oogonial cell undergoing mitotic prophase http://purl.obolibrary.org/obo/PLANA_0003232 metaphase oogonial cell http://purl.obolibrary.org/obo/PLANA_0000239 oogonial cell oogonial cell undergoing mitotic metaphase http://purl.obolibrary.org/obo/PLANA_0003233 anaphase oogonial cell http://purl.obolibrary.org/obo/PLANA_0000239 oogonial cell oogonial cell undergoing mitotic anaphase http://purl.obolibrary.org/obo/PLANA_0003234 telophase oogonial cell http://purl.obolibrary.org/obo/PLANA_0000239 oogonial cell oogonial cell undergoing mitotic telophase http://purl.obolibrary.org/obo/PLANA_0003235 G1 phase germ cell cyst http://purl.obolibrary.org/obo/PLANA_0002043 germ cell cyst germ cell cyst undergoing mitotic G1 phase http://purl.obolibrary.org/obo/PLANA_0003236 S phase germ cell cyst http://purl.obolibrary.org/obo/PLANA_0002043 germ cell cyst germ cell cyst undergoing mitotic S phase http://purl.obolibrary.org/obo/PLANA_0003237 G2 phase germ cell cyst http://purl.obolibrary.org/obo/PLANA_0002043 germ cell cyst germ cell cyst undergoing mitotic G2 phase http://purl.obolibrary.org/obo/PLANA_0003238 prophase germ cell cyst http://purl.obolibrary.org/obo/PLANA_0002043 germ cell cyst germ cell cyst undergoing mitotic prophase http://purl.obolibrary.org/obo/PLANA_0003239 metaphase germ cell cyst http://purl.obolibrary.org/obo/PLANA_0002043 germ cell cyst germ cell cyst undergoing mitotic metaphase http://purl.obolibrary.org/obo/PLANA_0003240 anaphase germ cell cyst http://purl.obolibrary.org/obo/PLANA_0002043 germ cell cyst germ cell cyst undergoing mitotic anaphase http://purl.obolibrary.org/obo/PLANA_0003241 telophase germ cell cyst http://purl.obolibrary.org/obo/PLANA_0002043 germ cell cyst germ cell cyst undergoing mitotic telophase http://purl.obolibrary.org/obo/PLANA_0003242 meiotic S phase spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing meiotic S phase http://purl.obolibrary.org/obo/PLANA_0003243 meiotic G1 phase spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing meiotic G1 phase http://purl.obolibrary.org/obo/PLANA_0003244 meiotic G2 phase spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing meiotic G2 phase http://purl.obolibrary.org/obo/PLANA_0003245 meiotic prophase I spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing meiotic prophase I http://purl.obolibrary.org/obo/PLANA_0003246 leptotene stage spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing leptotene http://purl.obolibrary.org/obo/PLANA_0003247 zygotene stage spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing zygotene http://purl.obolibrary.org/obo/PLANA_0003248 pachytene stage spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing pachytene http://purl.obolibrary.org/obo/PLANA_0003249 diplotene stage spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing diplotene http://purl.obolibrary.org/obo/PLANA_0003250 diakinesis stage spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing diakinesis http://purl.obolibrary.org/obo/PLANA_0003251 meiotic metaphase 1 stage spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing meiotic metaphase I http://purl.obolibrary.org/obo/PLANA_0003252 meiotic anaphase I stage spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing meiotic anaphase I http://purl.obolibrary.org/obo/PLANA_0003253 meiotic telophase I spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing meiotic telophase I http://purl.obolibrary.org/obo/PLANA_0003254 meiosis II stage spermatocyte http://purl.obolibrary.org/obo/PLANA_0000221 spermatocyte spermatocyte undergoing meiosis II cell cycle phase http://purl.obolibrary.org/obo/PLANA_0003255 meiotic prophase II spermatocyte http://purl.obolibrary.org/obo/PLANA_0003254 meiosis II stage spermatocyte spermatocyte undergoing meiotic prophase II http://purl.obolibrary.org/obo/PLANA_0003256 meiotic metaphase 2 spermatocyte http://purl.obolibrary.org/obo/PLANA_0003254 meiosis II stage spermatocyte spermatocyte undergoing meiotic metaphase II http://purl.obolibrary.org/obo/PLANA_0003257 meiotic anaphase II spermatocyte http://purl.obolibrary.org/obo/PLANA_0003254 meiosis II stage spermatocyte spermatocyte undergoing meiotic anaphase II http://purl.obolibrary.org/obo/PLANA_0003258 meiotic telophase II spermatocyte http://purl.obolibrary.org/obo/PLANA_0003254 meiosis II stage spermatocyte spermatocyte undergoing meiotic telophase II http://purl.obolibrary.org/obo/PLANA_0003300 cephalic ganglia primordium http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity This primordium develops into cephalic ganglia http://purl.obolibrary.org/obo/PLANA_0003301 eye primordium http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity This primordium develops into eye http://purl.obolibrary.org/obo/PLANA_0003302 pharynx primordium http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity This primordium develops into pharynx http://purl.obolibrary.org/obo/PLANA_0003303 pigment cup primordium http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity This primordium develops into optic cup http://purl.obolibrary.org/obo/PLANA_0003304 testis primordium http://purl.obolibrary.org/obo/PLANA_0003305 gonad primoridium This primordium develops into testis http://purl.obolibrary.org/obo/PLANA_0003305 gonad primoridium http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity This primordium develops into gonad http://purl.obolibrary.org/obo/PLANA_0003400 protonephridial lumen http://purl.obolibrary.org/obo/PLANA_0002053 lumen lumen which is part of the protonephridia http://purl.obolibrary.org/obo/PLANA_0003401 testis lumen http://purl.obolibrary.org/obo/PLANA_0002053 lumen lumen which is part of the testis http://purl.obolibrary.org/obo/PLANA_0003402 ovary lumen http://purl.obolibrary.org/obo/PLANA_0002053 lumen lumen which is part of the ovary http://purl.obolibrary.org/obo/PLANA_0003403 flame cell lumen http://purl.obolibrary.org/obo/PLANA_0003400 protonephridial lumen lumen which is part of the flame cell http://purl.obolibrary.org/obo/PLANA_0003500 cephalic ganglia progenitor cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity A progenitor cell that gives rise to one or more of the cell type(s) in the nervous system. http://purl.obolibrary.org/obo/PLANA_0003501 dorsal epidermis progenitor cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity A progenitor cell that gives rise to one or more of the cell type(s) in the dorsal epidermis. http://purl.obolibrary.org/obo/PLANA_0003502 optic cup progenitor cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity A progenitor cell that gives rise to optic cup cells of the eye. http://purl.obolibrary.org/obo/PLANA_0003503 ventral epidermis progenitor cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity A progenitor cell that gives rise to one or more of the cell type(s) in the epidermis. http://purl.obolibrary.org/obo/PLANA_0003600 head fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment derived from a prepharyngeal amputation encompassing the head. http://purl.obolibrary.org/obo/PLANA_0003601 trunk fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. http://purl.obolibrary.org/obo/PLANA_0003602 tail fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment derived from a postpharyngeal amputation encompassing the tail. http://purl.obolibrary.org/obo/PLANA_0003603 prepharyngeal fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. http://purl.obolibrary.org/obo/PLANA_0003604 postpharyngeal fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. http://purl.obolibrary.org/obo/PLANA_0003605 anterior fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment encompassing all or part of the anterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003606 posterior fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment encompassing all or part of the posterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003607 lateral fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. [SMR: a fragment that encompasses the side of the animal, not necessarily longituduinal, or parallel to the midline] http://purl.obolibrary.org/obo/PLANA_0003608 longitudinal fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment a fragment derived from an amputation parallel to the midline. http://purl.obolibrary.org/obo/PLANA_0003609 plug fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. http://purl.obolibrary.org/obo/PLANA_0003610 wedge fragment http://purl.obolibrary.org/obo/PLANA_0002128 fragment A piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. http://purl.obolibrary.org/obo/PLANA_0003700 dorsal region of head fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a fragment derived from a prepharyngeal amputation encompassing the head. http://purl.obolibrary.org/obo/PLANA_0003701 ventral region of head fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a fragment derived from a prepharyngeal amputation encompassing the head. http://purl.obolibrary.org/obo/PLANA_0003702 anterior region of head fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a fragment derived from a prepharyngeal amputation encompassing the head. http://purl.obolibrary.org/obo/PLANA_0003703 posterior region of head fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a fragment derived from a prepharyngeal amputation encompassing the head. http://purl.obolibrary.org/obo/PLANA_0003704 dorsal region of trunk fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. http://purl.obolibrary.org/obo/PLANA_0003705 ventral region of trunk fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. http://purl.obolibrary.org/obo/PLANA_0003706 anterior region of trunk fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. http://purl.obolibrary.org/obo/PLANA_0003707 posterior region of trunk fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. http://purl.obolibrary.org/obo/PLANA_0003708 dorsal region of tail fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a fragment derived from a postpharyngeal amputation encompassing the tail. http://purl.obolibrary.org/obo/PLANA_0003709 ventral region of tail fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a fragment derived from a postpharyngeal amputation encompassing the tail. http://purl.obolibrary.org/obo/PLANA_0003710 anterior region of tail fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a fragment derived from a postpharyngeal amputation encompassing the tail. http://purl.obolibrary.org/obo/PLANA_0003711 posterior region of tail fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a fragment derived from a postpharyngeal amputation encompassing the tail. http://purl.obolibrary.org/obo/PLANA_0003712 dorsal region of prepharyngeal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. http://purl.obolibrary.org/obo/PLANA_0003713 ventral region of prepharyngeal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. http://purl.obolibrary.org/obo/PLANA_0003714 anterior region of prepharyngeal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. http://purl.obolibrary.org/obo/PLANA_0003715 posterior region of prepharyngeal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. http://purl.obolibrary.org/obo/PLANA_0003716 dorsal region of postpharyngeal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. http://purl.obolibrary.org/obo/PLANA_0003717 ventral region of postpharyngeal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. http://purl.obolibrary.org/obo/PLANA_0003718 anterior region of postpharyngeal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. http://purl.obolibrary.org/obo/PLANA_0003719 posterior region of postpharyngeal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. http://purl.obolibrary.org/obo/PLANA_0003720 dorsal region of anterior fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a fragment encompassing all or part of the anterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003721 ventral region of anterior fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a fragment encompassing all or part of the anterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003722 anterior region of anterior fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a fragment encompassing all or part of the anterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003723 posterior region of anterior fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a fragment encompassing all or part of the anterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003724 dorsal region of posterior fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a fragment encompassing all or part of the posterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003725 ventral region of posterior fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a fragment encompassing all or part of the posterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003726 anterior region of posterior fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a fragment encompassing all or part of the posterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003727 posterior region of posterior fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a fragment encompassing all or part of the posterior region of the animal. http://purl.obolibrary.org/obo/PLANA_0003728 dorsal region of lateral fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. http://purl.obolibrary.org/obo/PLANA_0003729 ventral region of lateral fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. http://purl.obolibrary.org/obo/PLANA_0003730 anterior region of lateral fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. http://purl.obolibrary.org/obo/PLANA_0003731 posterior region of lateral fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. http://purl.obolibrary.org/obo/PLANA_0003732 dorsal region of longitudinal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a fragment derived from an amputation parallel to the midline. http://purl.obolibrary.org/obo/PLANA_0003733 ventral region of longitudinal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a fragment derived from an amputation parallel to the midline. http://purl.obolibrary.org/obo/PLANA_0003734 anterior region of longitudinal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a fragment derived from an amputation parallel to the midline. http://purl.obolibrary.org/obo/PLANA_0003735 posterior region of longitudinal fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a fragment derived from an amputation parallel to the midline. http://purl.obolibrary.org/obo/PLANA_0003736 dorsal region of plug fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. http://purl.obolibrary.org/obo/PLANA_0003737 ventral region of plug fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. http://purl.obolibrary.org/obo/PLANA_0003738 anterior region of plug fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. http://purl.obolibrary.org/obo/PLANA_0003739 posterior region of plug fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. http://purl.obolibrary.org/obo/PLANA_0003740 dorsal region of wedge fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. http://purl.obolibrary.org/obo/PLANA_0003741 ventral region of wedge fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The ventral region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. http://purl.obolibrary.org/obo/PLANA_0003742 anterior region of wedge fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. http://purl.obolibrary.org/obo/PLANA_0003743 posterior region of wedge fragment http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. http://purl.obolibrary.org/obo/PLANA_0003504 testis somatic gonadal cell progenitor cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity This progenitor cell develops into testis somatic gonadal cell http://purl.obolibrary.org/obo/PLANA_0003800 anterior photoreceptor neuron http://purl.obolibrary.org/obo/PLANA_0000017 photoreceptor neuron photoreceptor neuron is contained in the anterior region of the eye http://purl.obolibrary.org/obo/PLANA_0003801 posterior photoreceptor neuron http://purl.obolibrary.org/obo/PLANA_0000017 photoreceptor neuron photoreceptor neuron is contained in the posterior region of the eye http://purl.obolibrary.org/obo/PLANA_0007568 guidepost cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell A cell present near the brain and eye where photoreceptor axons form a bundle projecting out from the eye that are near axon choice points. Guidepost cells are positive for Arrestin, notum, fz5/8-4+, 6G10, and low levels of troponin, tropomyosin, colF-2 and mp-1. http://purl.obolibrary.org/obo/PLANA_0007569 NME cell http://purl.obolibrary.org/obo/PLANA_0007568 guidepost cell Guidepost cell associated with the visual circuit that are present near the eye, located along axons just anterior and ventral to the eye. Name acronym stands for notum+ muscle cell near eye. http://purl.obolibrary.org/obo/PLANA_0007570 NMC cell http://purl.obolibrary.org/obo/PLANA_0007569 NME cell Guidepost cell assocaited with the visual circuit, present at the axon choice point ventral, posterior to and slightly medial to the eye. Name acronym stands for notum+ muscle cells at the choice point. http://purl.obolibrary.org/obo/PLANA_0007571 NBC cell http://purl.obolibrary.org/obo/PLANA_0007570 NMC cell Guidepost cell present at the medial brain, ventral to the optic chiasm. Closely associated with photoreceptor axons during regneration. Name acronym stands for notum+ brain cells. http://purl.obolibrary.org/obo/PLANA_0007572 juvenile organism http://purl.obolibrary.org/obo/PLANA_0000136 whole organism A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype http://purl.obolibrary.org/obo/PLANA_0007558 fission plane http://purl.obolibrary.org/obo/BSPO_0000400 anatomical plane Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs. http://purl.obolibrary.org/obo/PLANA_0007546 TrpA+ neural progenitor cell http://purl.obolibrary.org/obo/PLANA_0000012 neural progenitor cell piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons. http://purl.obolibrary.org/obo/PLANA_0000111 proximal tubule epithelial cell http://purl.obolibrary.org/obo/PLANA_0000106 ciliated epithelial cell Ciliated epithelial cells that assemble into proximal tubules. http://purl.obolibrary.org/obo/PLANA_0000138 Hyman vesicle http://purl.obolibrary.org/obo/PLANA_0002137 intracellular granule PROG-2-5 positive granules that range in size from 0.5um to 1um present in epithelia and epithelia progenitor cells. These are distinct from rhabdites. http://purl.obolibrary.org/obo/PLANA_0000140 anterior region of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus. http://purl.obolibrary.org/obo/PLANA_0000141 dorsal region of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes. http://purl.obolibrary.org/obo/PLANA_0000142 posterior region of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Three dimensional compartment along the anteroposterior axis that is closer to the tail rather than the head, from the anterior boundary of the pharyngeal pouch to the tip of the tail. http://purl.obolibrary.org/obo/PLANA_0000143 ventral region of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity Compartment along the dorsoventral axis that is below the anteroposterior axis. http://purl.obolibrary.org/obo/GO_0000003 reproduction http://purl.obolibrary.org/obo/GO_0008150 biological_process The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. http://purl.obolibrary.org/obo/GO_0000080 mitotic G1 phase http://purl.obolibrary.org/obo/GO_0051318 G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis. http://purl.obolibrary.org/obo/GO_0000084 mitotic S phase http://purl.obolibrary.org/obo/GO_0051320 S phase The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle. http://purl.obolibrary.org/obo/GO_0000085 mitotic G2 phase http://purl.obolibrary.org/obo/GO_0051319 G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis. http://purl.obolibrary.org/obo/GO_0000087 mitotic M phase http://purl.obolibrary.org/obo/GO_0098763 mitotic cell cycle phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle. http://purl.obolibrary.org/obo/GO_0000088 mitotic prophase http://purl.obolibrary.org/obo/GO_0051324 prophase The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. http://purl.obolibrary.org/obo/GO_0000089 mitotic metaphase http://purl.obolibrary.org/obo/GO_0051323 metaphase The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle. http://purl.obolibrary.org/obo/GO_0000090 mitotic anaphase http://purl.obolibrary.org/obo/GO_0051322 anaphase The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle. http://purl.obolibrary.org/obo/GO_0000093 mitotic telophase http://purl.obolibrary.org/obo/GO_0051326 telophase The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. http://purl.obolibrary.org/obo/GO_0000237 leptotene http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible. http://purl.obolibrary.org/obo/GO_0000238 zygotene http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase The cell cycle phase which follows leptotene during prophase I of meiosis, and during which each chromosome pairs with its homolog; the two become aligned and crossing over may occur. http://purl.obolibrary.org/obo/GO_0000239 pachytene http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase The cell cycle phase which follows zygotene during prophase I of meiosis, and during which crossing over occurs between a chromatid in one partner and another chromatid in the homologous chromosome. http://purl.obolibrary.org/obo/GO_0000240 diplotene http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase The cell cycle phase which follows pachytene during prophase I of meiosis, during which the homologous chromosomes begin to separate and the synaptonemal complex dissolves. http://purl.obolibrary.org/obo/GO_0000241 diakinesis http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred. http://purl.obolibrary.org/obo/GO_0000278 mitotic cell cycle http://purl.obolibrary.org/obo/GO_0007049 cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. http://purl.obolibrary.org/obo/GO_0000279 M phase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase. http://purl.obolibrary.org/obo/GO_0000280 nuclear division http://purl.obolibrary.org/obo/GO_0048285 organelle fission The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. http://purl.obolibrary.org/obo/GO_0003006 developmental process involved in reproduction http://purl.obolibrary.org/obo/GO_0032502 developmental process A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. http://purl.obolibrary.org/obo/GO_0003674 molecular_function http://purl.obolibrary.org/obo/BFO_0000015 process A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. http://purl.obolibrary.org/obo/GO_0007049 cell cycle http://purl.obolibrary.org/obo/GO_0009987 cellular process The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. http://purl.obolibrary.org/obo/GO_0007128 meiotic prophase I http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase The cell cycle phase which is the first stage of meiosis I and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. http://purl.obolibrary.org/obo/GO_0008150 biological_process http://purl.obolibrary.org/obo/BFO_0000015 process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. http://purl.obolibrary.org/obo/GO_0009987 cellular process http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. http://purl.obolibrary.org/obo/GO_0016301 kinase activity http://purl.obolibrary.org/obo/GO_0016772 transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. http://purl.obolibrary.org/obo/GO_0019953 sexual reproduction http://purl.obolibrary.org/obo/GO_0000003 reproduction A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). http://purl.obolibrary.org/obo/GO_0022402 cell cycle process http://purl.obolibrary.org/obo/GO_0009987 cellular process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase http://purl.obolibrary.org/obo/GO_0044848 biological phase One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. http://purl.obolibrary.org/obo/GO_0022414 reproductive process http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. http://purl.obolibrary.org/obo/GO_0032502 developmental process http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. http://purl.obolibrary.org/obo/GO_0044848 biological phase http://purl.obolibrary.org/obo/GO_0008150 biological_process A distinct period or stage in a biological process or cycle. http://purl.obolibrary.org/obo/GO_0048285 organelle fission http://purl.obolibrary.org/obo/GO_0006996 organelle organization The creation of two or more organelles by division of one organelle. http://purl.obolibrary.org/obo/GO_0048856 anatomical structure development http://purl.obolibrary.org/obo/GO_0032502 developmental process The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. http://purl.obolibrary.org/obo/GO_0051301 cell division http://purl.obolibrary.org/obo/GO_0009987 cellular process The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. http://purl.obolibrary.org/obo/GO_0051318 G1 phase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis. http://purl.obolibrary.org/obo/GO_0051319 G2 phase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis). http://purl.obolibrary.org/obo/GO_0051320 S phase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase The cell cycle phase, following G1, during which DNA synthesis takes place. http://purl.obolibrary.org/obo/GO_0051321 meiotic cell cycle http://purl.obolibrary.org/obo/GO_0022414 reproductive process Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. http://purl.obolibrary.org/obo/GO_0051322 anaphase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle. http://purl.obolibrary.org/obo/GO_0051323 metaphase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell. http://purl.obolibrary.org/obo/GO_0051324 prophase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. http://purl.obolibrary.org/obo/GO_0051326 telophase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. http://purl.obolibrary.org/obo/GO_0051329 mitotic interphase http://purl.obolibrary.org/obo/GO_0098763 mitotic cell cycle phase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs. http://purl.obolibrary.org/obo/GO_0098763 mitotic cell cycle phase http://purl.obolibrary.org/obo/GO_0022403 cell cycle phase One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. http://purl.obolibrary.org/obo/GO_0098764 meiosis I cell cycle phase http://purl.obolibrary.org/obo/GO_0098762 meiotic cell cycle phase A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs. http://purl.obolibrary.org/obo/GO_1903046 meiotic cell cycle process http://purl.obolibrary.org/obo/GO_0022414 reproductive process A process that is part of the meiotic cell cycle. http://purl.obolibrary.org/obo/GO_1903047 mitotic cell cycle process http://purl.obolibrary.org/obo/GO_0022402 cell cycle process A process that is part of the mitotic cell cycle. http://purl.obolibrary.org/obo/GO_0043473 pigmentation http://purl.obolibrary.org/obo/GO_0008150 biological_process The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. http://purl.obolibrary.org/obo/GO_0051328 meiotic interphase http://purl.obolibrary.org/obo/GO_0098762 meiotic cell cycle phase The cell cycle phase which begins after cytokinesis and ends when meiotic prophase begins. Meiotic cells have an interphase after each meiotic division, but only interphase I involves replication of the cell's DNA. http://purl.obolibrary.org/obo/PLANA_0003004 prepharyngeal midline http://purl.obolibrary.org/obo/BFO_0000040 material entity The center-most region just anterior to the pharynx http://purl.obolibrary.org/obo/PLANA_0004000 regenerating head fragment http://purl.obolibrary.org/obo/PLANA_0003600 head fragment a head fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004001 regenerating trunk fragment http://purl.obolibrary.org/obo/PLANA_0003601 trunk fragment a trunk fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004002 regenerating tail fragment http://purl.obolibrary.org/obo/PLANA_0003602 tail fragment a tail fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004003 regenerating prepharyngeal fragment http://purl.obolibrary.org/obo/PLANA_0003603 prepharyngeal fragment a prepharyngeal fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004004 regenerating postpharyngeal fragment http://purl.obolibrary.org/obo/PLANA_0003604 postpharyngeal fragment a postpharyngeal fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004005 regenerating anterior fragment http://purl.obolibrary.org/obo/PLANA_0003605 anterior fragment a anterior fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004006 regenerating posterior fragment http://purl.obolibrary.org/obo/PLANA_0003606 posterior fragment a posterior fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004007 regenerating lateral fragment http://purl.obolibrary.org/obo/PLANA_0003607 lateral fragment a lateral fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004008 regenerating longitudinal fragment http://purl.obolibrary.org/obo/PLANA_0003608 longitudinal fragment a longitudinal fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004009 regenerating plug fragment http://purl.obolibrary.org/obo/PLANA_0003609 plug fragment a plug fragment that is regenerating http://purl.obolibrary.org/obo/PLANA_0004010 regenerating wedge fragment http://purl.obolibrary.org/obo/PLANA_0003610 wedge fragment a wedge fragment that is regenerating http://purl.obolibrary.org/obo/GO_0071840 cellular component organization or biogenesis http://purl.obolibrary.org/obo/GO_0009987 cellular process A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. http://purl.obolibrary.org/obo/PLANA_0003306 ovary primordium http://purl.obolibrary.org/obo/PLANA_0003305 gonad primoridium This primordium develops into ovary http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity http://purl.obolibrary.org/obo/CARO_0030000 biological entity A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. http://purl.obolibrary.org/obo/CARO_0000003 anatomical structure http://purl.obolibrary.org/obo/CARO_0000006 material anatomical entity Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. http://purl.obolibrary.org/obo/CARO_0000006 material anatomical entity http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity An anatomical entity that has mass. http://purl.obolibrary.org/obo/CARO_0000007 immaterial anatomical entity http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity An anatomical entity that has no mass. http://purl.obolibrary.org/obo/CARO_0000008 anatomical line http://purl.obolibrary.org/obo/CARO_0000007 immaterial anatomical entity A one dimensional, immaterial anatomical entity. http://purl.obolibrary.org/obo/CARO_0000010 anatomical boundary http://purl.obolibrary.org/obo/CARO_0000007 immaterial anatomical entity A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. http://purl.obolibrary.org/obo/PLANA_0007552 nu neoblast http://purl.obolibrary.org/obo/PLANA_0000012 neural progenitor cell A population of piwi-2+, ston-2+, elav-2+, ptprd-9+ and msi-1+ progenitors that give rise to one or more neuronal (pc-2+, synapsin+) lineages. http://purl.obolibrary.org/obo/PLANA_0007559 ovary nerve plexus http://purl.obolibrary.org/obo/BFO_0000040 material entity Nerve plexus surrounding the ovary. http://purl.obolibrary.org/obo/PLANA_0000134 longitudinal muscle progenitor cell http://purl.obolibrary.org/obo/PLANA_0000019 muscle progenitor cell piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers. http://purl.obolibrary.org/obo/PLANA_0007555 pax3/7+ neural progenitor cell http://purl.obolibrary.org/obo/PLANA_0000012 neural progenitor cell piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons. http://purl.obolibrary.org/obo/PLANA_0007561 head margin http://purl.obolibrary.org/obo/PLANA_0000043 dorsal ventral margin of the whole animal Peripheral region of the head. http://purl.obolibrary.org/obo/PLANA_0007538 adhesion gland http://purl.obolibrary.org/obo/PLANA_0000113 tissue Groupings of specialized epithelial cells located along the dorsal ventral margin. Adhesion glands are comprised of three cell types, the viscid and releasing gland cells which penetrate through an epithelial anchor cell and terminate at the epidermal surface. http://purl.obolibrary.org/obo/PLANA_0003002 anterior region of the eye http://purl.obolibrary.org/obo/BFO_0000040 material entity The anterior region of the eye. http://purl.obolibrary.org/obo/PLANA_0003003 posterior region of the eye http://purl.obolibrary.org/obo/BFO_0000040 material entity The posterior region of the eye. http://purl.obolibrary.org/obo/PLANA_0004511 oral-aboral axis of the embryo http://purl.obolibrary.org/obo/BFO_0000040 material entity Axis that runs from the oral pole and to the aboral pole of the spherical embryo (Stage 3 through early Stage 6). The oral pole is centered around the embryonic pharynx; the aboral pole is located opposite the embryonic pharynx. http://purl.obolibrary.org/obo/PLANA_0004512 primitive ectoderm surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface The apical surface of the single layered primitive ectoderm that is in contact with the environment. http://purl.obolibrary.org/obo/PLANA_0004513 primtive gut cell surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface The surface of the primitive gut cells in contact with the embryonic wall. http://purl.obolibrary.org/obo/PLANA_0004514 embryonic gut cell surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface The surface of phagocytic embryonic gut cells in contact with ingested yolk cells. http://purl.obolibrary.org/obo/PLANA_0004516 embryonic pharynx lumen epithelial surface http://purl.obolibrary.org/obo/BSPO_0000005 anatomical surface The epithelial cell surface lining the embryonic pharynx lumen. http://purl.obolibrary.org/obo/PLANA_0004517 blastomere http://purl.obolibrary.org/obo/PLANA_0000123 embryonic cell An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. Blastomeres give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5. http://purl.obolibrary.org/obo/PLANA_0004518 extraembryonic cell http://purl.obolibrary.org/obo/PLANA_0000119 terminally differentiated cell Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues. http://purl.obolibrary.org/obo/PLANA_0004519 embryonic pharynx neuron http://purl.obolibrary.org/obo/PLANA_0004518 extraembryonic cell A neuronal cell innervating the embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening. http://purl.obolibrary.org/obo/PLANA_0004520 embryonic pharynx radial muscle cell http://purl.obolibrary.org/obo/PLANA_0004518 extraembryonic cell Differentiated radial muscle cell present in the embryonic pharynx. http://purl.obolibrary.org/obo/PLANA_0004521 embryonic pharynx epithelial cell http://purl.obolibrary.org/obo/PLANA_0004518 extraembryonic cell foxA1+ epithelial cell contained in the embryonic pharynx. http://purl.obolibrary.org/obo/PLANA_0004524 embryonic pharynx circular muscle cell http://purl.obolibrary.org/obo/PLANA_0004518 extraembryonic cell Differentiated muscle cell present in a circular muscle fiber of the embryonic pharynx. http://purl.obolibrary.org/obo/PLANA_0004527 copulatory region http://purl.obolibrary.org/obo/PLANA_0000102 anatomical region Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus. http://purl.obolibrary.org/obo/PLANA_0004528 pharynx epithelium http://purl.obolibrary.org/obo/PLANA_0002118 epithelium Epithelia associated with the pharynx organ. http://purl.obolibrary.org/obo/PLANA_0004529 integumental system http://purl.obolibrary.org/obo/PLANA_0000114 anatomical system Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. http://purl.obolibrary.org/obo/PLANA_0004530 oviduct lumen http://purl.obolibrary.org/obo/PLANA_0002053 lumen Anatomical space enclosed by the oviduct epithelium. http://purl.obolibrary.org/obo/PLANA_0004531 sperm duct lumen http://purl.obolibrary.org/obo/PLANA_0002053 lumen Anatomical space enclosed by the sperm duct epithelium. http://purl.obolibrary.org/obo/PLANA_0004532 oviduct epithelium http://purl.obolibrary.org/obo/PLANA_0002023 ciliated epithelium Ciliated epithelium lining the oviduct. http://purl.obolibrary.org/obo/PLANA_0004533 sperm duct epithelium http://purl.obolibrary.org/obo/PLANA_0002023 ciliated epithelium Ciliated epithelium lining the sperm duct. http://purl.obolibrary.org/obo/PLANA_0004534 tuba lumen http://purl.obolibrary.org/obo/PLANA_0002053 lumen Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct. http://purl.obolibrary.org/obo/PLANA_0007539 anchor cell http://purl.obolibrary.org/obo/BFO_0000040 material entity Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells. http://purl.obolibrary.org/obo/PLANA_0007540 viscid gland cell http://purl.obolibrary.org/obo/BFO_0000040 material entity A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate. http://purl.obolibrary.org/obo/PLANA_0007541 releasing gland cell http://purl.obolibrary.org/obo/BFO_0000040 material entity Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance. http://purl.obolibrary.org/obo/PLANA_0000115 distal tubule epithelial cell http://purl.obolibrary.org/obo/PLANA_0000015 non ciliated epithelial cell Nonciliated epithelial cells that assemble into protonephridial distal tubules. http://purl.obolibrary.org/obo/PATO_0040012 plug shaped http://purl.obolibrary.org/obo/PATO_0000052 shape A shape that is in the form of a plug, being tube-like and expanded on one end. http://purl.obolibrary.org/obo/PLANA_0003001 lateral region of the whole animal http://purl.obolibrary.org/obo/BFO_0000040 material entity The lateral region of the medio-lateral axis of the whole animal. http://purl.obolibrary.org/obo/PLANA_0003900 head blastema http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity blastema which develops into head region http://purl.obolibrary.org/obo/PLANA_0003901 tail blastema http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity blastema which develops into tail region http://purl.obolibrary.org/obo/PLANA_0007564 sexual organism http://purl.obolibrary.org/obo/PLANA_0000136 whole organism An individual member of the sexual biotype of Schmidtea mediterranea. http://purl.obolibrary.org/obo/PLANA_0007565 asexual organism http://purl.obolibrary.org/obo/PLANA_0000136 whole organism An individual member of the asexual biotype of Schmidtea mediterranea. http://purl.obolibrary.org/obo/PLANA_0000027 Smed sexual biotype http://purl.obolibrary.org/obo/PLANA_0000021 biotype Strains of cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids. http://purl.obolibrary.org/obo/PLANA_0000013 visceral musculature http://purl.obolibrary.org/obo/PLANA_0000431 organ Musculature surrounding internal organs of the body. http://purl.obolibrary.org/obo/PLANA_0000015 non ciliated epithelial cell http://purl.obolibrary.org/obo/PLANA_0000100 epithelial cell An epithelial cell lacking cilia. http://purl.obolibrary.org/obo/PLANA_0000024 Smed asexual biotype http://purl.obolibrary.org/obo/PLANA_0000021 biotype Asexual animal strains that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed. http://purl.obolibrary.org/obo/PLANA_0000130 circular muscle progenitor cell http://purl.obolibrary.org/obo/PLANA_0002095 somatic cell piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers. http://purl.obolibrary.org/obo/PLANA_0007544 cintillo+ sensory neuron http://purl.obolibrary.org/obo/BFO_0000040 material entity A subset of sensory neurons located along the dorsal head margin. http://purl.obolibrary.org/obo/PLANA_0007548 transverse commissure http://purl.obolibrary.org/obo/PLANA_0002025 commissure Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords. http://purl.obolibrary.org/obo/PLANA_0007551 klf+ sensory neuron progenitor cell http://purl.obolibrary.org/obo/PLANA_0000012 neural progenitor cell piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons. http://purl.obolibrary.org/obo/PLANA_0007553 lateral nerve http://purl.obolibrary.org/obo/PLANA_0000113 tissue A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus. http://purl.obolibrary.org/obo/PLANA_0007557 testis nerve plexus http://purl.obolibrary.org/obo/BFO_0000040 material entity Nerve plexus surrounding the testis. http://purl.obolibrary.org/obo/PLANA_0000136 whole organism http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure Anatomical structure that is an individual member of Schmidtea mediterranea or any other flatworm of the class Turbellaria. http://purl.obolibrary.org/obo/PLANA_0000137 regeneration http://purl.obolibrary.org/obo/GO_0048856 anatomical structure development The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). http://purl.obolibrary.org/obo/PLANA_0000135 female primordial germ cell http://purl.obolibrary.org/obo/PLANA_0000121 stem cell Cells expressing nanos that are located ventrally in the location that the ovaries form. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with oogonial stem cell. http://purl.obolibrary.org/obo/PLANA_0003000 dorsal region of tail http://purl.obolibrary.org/obo/BFO_0000040 material entity The dorsal region of the tail. http://purl.obolibrary.org/obo/PLANA_0007563 glutamatergic neuron http://purl.obolibrary.org/obo/BFO_0000004 independent continuant Neurons that express the biogenic amine glutamate. http://purl.obolibrary.org/obo/PLANA_0003802 lateral muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell muscle cell is contained in the lateral region http://purl.obolibrary.org/obo/PLANA_0003803 anterior muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell muscle cell is contained in the anterior region http://purl.obolibrary.org/obo/PLANA_0003804 posterior muscle cell http://purl.obolibrary.org/obo/PLANA_0000101 muscle cell muscle cell is contained in the posterior region http://purl.obolibrary.org/obo/PLANA_0007566 non-ciliated neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron A neuron cell that does not have cilia. http://purl.obolibrary.org/obo/PLANA_0007567 cilated neuron http://purl.obolibrary.org/obo/PLANA_0000099 neuron A neuron that has cilia. http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/CARO_0030000 biological entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000019 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/UBERON_0005423 developing anatomical structure http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity http://purl.obolibrary.org/obo/BSPO_0000066 lateral side http://purl.obolibrary.org/obo/BSPO_0000054 anatomical side http://purl.obolibrary.org/obo/BSPO_0000094 dorsal/ventral compartment boundary http://purl.obolibrary.org/obo/BSPO_0000092 anatomical compartment boundary http://purl.obolibrary.org/obo/GO_0003824 catalytic activity http://purl.obolibrary.org/obo/GO_0003674 molecular_function http://purl.obolibrary.org/obo/GO_0016740 transferase activity http://purl.obolibrary.org/obo/GO_0003824 catalytic activity http://purl.obolibrary.org/obo/GO_0016772 transferase activity, transferring phosphorus-containing groups http://purl.obolibrary.org/obo/GO_0016740 transferase activity http://purl.obolibrary.org/obo/BSPO_0000086 anatomical compartment http://purl.obolibrary.org/obo/CARO_0000003 anatomical structure http://purl.obolibrary.org/obo/BSPO_0000092 anatomical compartment boundary http://purl.obolibrary.org/obo/CARO_0000010 anatomical boundary http://purl.obolibrary.org/obo/PLANA_0000021 biotype Organisms sharing a specified genotype or karyotype. http://purl.obolibrary.org/obo/GO_0005575 cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. http://purl.obolibrary.org/obo/UBERON_0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. http://purl.obolibrary.org/obo/PLANA_0002122 perturbation An event or occurrence that causes damage to a tissue or organ. http://purl.obolibrary.org/obo/PLANA_0003101 ventral epidermis cell cell which is part of the ventral epidermis http://purl.obolibrary.org/obo/PLANA_0003102 visual system cell cell which is part of the visual system http://purl.obolibrary.org/obo/PLANA_0003105 dorsal epidermis cell cell which is part of the dorsal region of the epidermis http://purl.obolibrary.org/obo/PLANA_0003106 adhesion gland cell cell which is part of the adhesion gland http://purl.obolibrary.org/obo/PLANA_0003107 body wall muscle cell cell which is part of the body wall musculature http://purl.obolibrary.org/obo/PLANA_0003109 anterior pole cell cell which is part of the anterior pole http://purl.obolibrary.org/obo/PLANA_0003115 ommochrome pigment granule pigment granule which is part of the ommochrome pigment cell http://purl.obolibrary.org/obo/PLANA_0003116 parenchymal cell cell which is part of the parenchyma http://purl.obolibrary.org/obo/PLANA_0003117 parapharyngeal cell cell which is part of the parapharyngeal region http://purl.obolibrary.org/obo/PLANA_0003118 prepharyngeal cell cell which is part of the prepharyngeal region http://purl.obolibrary.org/obo/PLANA_0000425 obsolete definitive anatomical structure http://purl.obolibrary.org/obo/PLANA_0000132 obsolete gametogenesis http://purl.obolibrary.org/obo/PLANA_0000209 obsolete developing anatomical structure http://purl.obolibrary.org/obo/PLANA_0000212 obsolete blastomere compartment http://purl.obolibrary.org/obo/PLANA_0000225 obsolete oviparity http://purl.obolibrary.org/obo/PLANA_0000226 obsolete cross-fertilization http://purl.obolibrary.org/obo/PLANA_0000242 obsolete anatomical cavity http://purl.obolibrary.org/obo/PLANA_0000400 obsolete anatomical entity http://purl.obolibrary.org/obo/PLANA_0000401 obsolete immaterial anatomical entity http://purl.obolibrary.org/obo/PLANA_0000402 obsolete anatomical point http://purl.obolibrary.org/obo/PLANA_0000403 obsolete anatomical space http://purl.obolibrary.org/obo/PLANA_0000416 obsolete organism subdivision http://purl.obolibrary.org/obo/PLANA_0000424 obsolete material anatomical entity http://purl.obolibrary.org/obo/PLANA_0000426 obsolete acellular anatomical structure http://purl.obolibrary.org/obo/PLANA_0000432 obsolete regenerating anatomical structure http://purl.obolibrary.org/obo/PLANA_0000433 obsolete cellular component http://purl.obolibrary.org/obo/PLANA_0000489 obsolete anatomical line http://purl.obolibrary.org/obo/PLANA_0000490 obsolete anatomical plane http://purl.obolibrary.org/obo/PLANA_0000491 obsolete plane of autotomy http://purl.obolibrary.org/obo/PLANA_0000493 obsolete nervous system commissure http://purl.obolibrary.org/obo/PLANA_0000496 obsolete anatomical boundary http://purl.obolibrary.org/obo/PLANA_0000497 obsolete anatomical junction http://purl.obolibrary.org/obo/PLANA_0000498 obsolete main body axis http://purl.obolibrary.org/obo/PLANA_0000500 obsolete cell part http://purl.obolibrary.org/obo/PLANA_0000503 obsolete cilium http://purl.obolibrary.org/obo/PLANA_0000511 obsolete acidophilic cytoplasm http://purl.obolibrary.org/obo/PLANA_0000512 obsolete basophilic cytoplasm http://purl.obolibrary.org/obo/PLANA_0000516 obsolete cytoskeleton organization http://purl.obolibrary.org/obo/PLANA_0007502 obsolete coronal plane http://purl.obolibrary.org/obo/PLANA_0007504 obsolete dorsal compartment http://purl.obolibrary.org/obo/PLANA_0007505 obsolete ventral compartment http://purl.obolibrary.org/obo/PLANA_0007506 obsolete anterior compartment http://purl.obolibrary.org/obo/PLANA_0007507 obsolete posterior compartment http://purl.obolibrary.org/obo/PLANA_0007508 obsolete extracellular component http://purl.obolibrary.org/obo/PLANA_0007536 obsolete specific_to http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/PLANA_0000037 obsolete definitive tissue http://purl.obolibrary.org/obo/PLANA_0000040 obsolete Schmidtea mediterranea developmental stage http://purl.obolibrary.org/obo/PLANA_0000051 obsolete direct development http://purl.obolibrary.org/obo/PLANA_0000052 obsolete dispersed cleavage http://purl.obolibrary.org/obo/PLANA_0000057 obsolete embryonic cleavage http://purl.obolibrary.org/obo/PLANA_0000086 obsolete protosphere http://purl.obolibrary.org/obo/PLANA_0000091 obsolete sphere formation http://purl.obolibrary.org/obo/PLANA_0000094 obsolete tissue morphogenesis http://purl.obolibrary.org/obo/PLANA_0000109 obsolete anatomical compartment subdivision feature http://purl.obolibrary.org/obo/PLANA_0000112 obsolete Schmidtea mediterranea developmental term http://purl.obolibrary.org/obo/PLANA_0000129 obsolete anatomical structure http://purl.obolibrary.org/obo/PLANA_0000082 obsolete racing stripe http://purl.obolibrary.org/obo/PLANA_0007554 obsolete parenchymal compartment http://purl.obolibrary.org/obo/PLANA_0007545 obsolete epidermal compartment http://purl.obolibrary.org/obo/PLANA_0007537 obsolete brain http://purl.obolibrary.org/obo/PLANA_0007549 obsolete body wall musculature compartment http://purl.obolibrary.org/obo/PLANA_0002117 obsolete oblique http://purl.obolibrary.org/obo/PLANA_0007560 obsolete gastrovascular compartment http://purl.obolibrary.org/obo/RO_0000052 characteristic of http://purl.obolibrary.org/obo/RO_0002314 characteristic of part of inheres_in a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. http://purl.obolibrary.org/obo/RO_0000079 function of http://purl.obolibrary.org/obo/RO_0000052 characteristic of is function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000080 quality of http://purl.obolibrary.org/obo/RO_0000052 characteristic of quality_of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000085 has function http://purl.obolibrary.org/obo/RO_0000053 has characteristic has_function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000086 has quality http://purl.obolibrary.org/obo/RO_0000053 has characteristic has_quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/BFO_0000051 has_part http://purl.obolibrary.org/obo/RO_0002131 overlaps has_part a core relation that holds between a whole and its part http://purl.obolibrary.org/obo/RO_0000087 has role http://purl.obolibrary.org/obo/RO_0000053 has characteristic has_role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002327 enables http://purl.obolibrary.org/obo/RO_0002215 capable of is executing c enables p iff c is capable of p and c acts to execute p. http://purl.obolibrary.org/obo/RO_0002409 indirectly negatively regulates http://purl.obolibrary.org/obo/RO_0012012 indirectly regulates indirectly inhibits p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. http://purl.obolibrary.org/obo/RO_0002436 molecularly interacts with http://purl.obolibrary.org/obo/RO_0002434 interacts with molecularly binds with An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. http://purl.obolibrary.org/obo/RO_0002449 directly negatively regulates activity of http://purl.obolibrary.org/obo/RO_0002448 directly regulates activity of directly inhibits The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. http://purl.obolibrary.org/obo/BFO_0000062 preceded by http://purl.obolibrary.org/obo/RO_0002086 ends after preceded_by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. http://purl.obolibrary.org/obo/RO_0000081 role of http://purl.obolibrary.org/obo/RO_0000052 characteristic of role_of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/BFO_0000050 part_of http://purl.obolibrary.org/obo/RO_0002131 overlaps part_of a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/RO_0002233 has input http://purl.obolibrary.org/obo/RO_0000057 has participant consumes p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. http://purl.obolibrary.org/obo/RO_0002314 characteristic of part of http://purl.obolibrary.org/obo/RO_0002502 depends on inheres in part of q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. http://purl.obolibrary.org/obo/RO_0002215 capable of http://purl.obolibrary.org/obo/RO_0002216 capable of part of has function realized in A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. http://purl.obolibrary.org/obo/RO_0002331 involved in http://purl.obolibrary.org/obo/RO_0002431 involved in or involved in regulation of enables part of c involved_in p if and only if c enables some process p', and p' is part of p http://purl.obolibrary.org/obo/RO_0002431 involved in or involved in regulation of http://purl.obolibrary.org/obo/RO_0002500 causal agent in process involved in or reguates c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p http://purl.obolibrary.org/obo/RO_0002216 capable of part of http://purl.obolibrary.org/obo/RO_0002500 causal agent in process has function in c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. http://purl.obolibrary.org/obo/RO_0002329 part of structure that is capable of http://purl.obolibrary.org/obo/RO_0002328 functionally related to 0 this relation holds between c and p when c is part of some c', and c' is capable of p. http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes influences (processual) p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. http://purl.obolibrary.org/obo/RO_0002407 indirectly positively regulates http://purl.obolibrary.org/obo/RO_0012012 indirectly regulates indirectly activates p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. http://purl.obolibrary.org/obo/RO_0002432 is active in http://purl.obolibrary.org/obo/RO_0002328 functionally related to executes activity in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. http://purl.obolibrary.org/obo/RO_0002450 directly positively regulates activity of http://purl.obolibrary.org/obo/RO_0002448 directly regulates activity of directly activates The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. http://purl.obolibrary.org/obo/RO_0002025 has effector activity http://purl.obolibrary.org/obo/RO_0002017 has component activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. http://purl.obolibrary.org/obo/RO_0002258 developmentally preceded by http://purl.obolibrary.org/obo/RO_0002324 developmentally related to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p http://purl.obolibrary.org/obo/RO_0002286 developmentally succeeded by http://purl.obolibrary.org/obo/RO_0002384 has developmental potential involving Inverse of developmentally preceded by http://purl.obolibrary.org/obo/RO_0002384 has developmental potential involving http://purl.obolibrary.org/obo/RO_0002324 developmentally related to x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). http://purl.obolibrary.org/obo/RO_0002388 has potential to directly develop into http://purl.obolibrary.org/obo/RO_0002387 has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y http://purl.obolibrary.org/obo/RO_0002571 lumen of http://purl.obolibrary.org/obo/BFO_0000050 part_of x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. http://purl.obolibrary.org/obo/BFO_0000063 precedes http://purl.obolibrary.org/obo/RO_0002222 temporally related to x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. http://purl.obolibrary.org/obo/IAO_0000219 denotes http://purl.obolibrary.org/obo/IAO_0000136 is about A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically http://purl.obolibrary.org/obo/OBI_0000299 has_specified_output http://purl.obolibrary.org/obo/RO_0000057 has participant The inverse property of is_specified_output_of http://purl.obolibrary.org/obo/OBI_0000312 is_specified_output_of http://purl.obolibrary.org/obo/RO_0000056 participates in A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/RO_0002220 adjacent to http://purl.obolibrary.org/obo/RO_0002163 spatially disjoint from x adjacent to y if and only if x and y share a boundary. http://purl.obolibrary.org/obo/RO_0002018 has component process http://purl.obolibrary.org/obo/RO_0002180 has component w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. http://purl.obolibrary.org/obo/RO_0019000 regulates characteristic http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. http://purl.obolibrary.org/obo/RO_0019001 positively regulates characteristic http://purl.obolibrary.org/obo/RO_0019000 regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. http://purl.obolibrary.org/obo/RO_0019002 negatively regulates characteristic http://purl.obolibrary.org/obo/RO_0019000 regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. http://purl.obolibrary.org/obo/RO_0002202 develops from http://purl.obolibrary.org/obo/RO_0002258 developmentally preceded by x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y http://purl.obolibrary.org/obo/RO_0002333 enabled by http://purl.obolibrary.org/obo/RO_0002328 functionally related to inverse of enables http://purl.obolibrary.org/obo/RO_0002404 causally downstream of http://purl.obolibrary.org/obo/RO_0002427 causally downstream of or within inverse of upstream of http://purl.obolibrary.org/obo/RO_0002412 immediately causally upstream of http://purl.obolibrary.org/obo/RO_0002411 causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. http://purl.obolibrary.org/obo/RO_0002448 directly regulates activity of http://purl.obolibrary.org/obo/RO_0011002 regulates activity of The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. http://purl.obolibrary.org/obo/RO_0002566 causally influences http://purl.obolibrary.org/obo/RO_0002506 causal relation between entities The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). http://purl.obolibrary.org/obo/RO_0002490 existence overlaps http://purl.obolibrary.org/obo/RO_0002487 relation between physical entity and a process or stage x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) http://purl.obolibrary.org/obo/RO_0002263 acts upstream of http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. http://purl.obolibrary.org/obo/RO_0002304 causally upstream of, positive effect http://purl.obolibrary.org/obo/RO_0004047 causally upstream of or within, positive effect p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. http://purl.obolibrary.org/obo/RO_0002305 causally upstream of, negative effect http://purl.obolibrary.org/obo/RO_0004046 causally upstream of or within, negative effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. http://purl.obolibrary.org/obo/RO_0002131 overlaps http://purl.obolibrary.org/obo/RO_0002323 mereotopologically related to x overlaps y iff they have some part in common. http://purl.obolibrary.org/obo/RO_0002254 has developmental contribution from http://purl.obolibrary.org/obo/RO_0002258 developmentally preceded by x has developmental contribution from y iff x has some part z such that z develops from y http://purl.obolibrary.org/obo/RO_0002496 existence starts during or after http://purl.obolibrary.org/obo/RO_0002487 relation between physical entity and a process or stage x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). http://purl.obolibrary.org/obo/RO_0002497 existence ends during or before http://purl.obolibrary.org/obo/RO_0002487 relation between physical entity and a process or stage x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. http://purl.obolibrary.org/obo/RO_0000091 has disposition http://purl.obolibrary.org/obo/RO_0000053 has characteristic a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000092 disposition of http://purl.obolibrary.org/obo/RO_0000052 characteristic of inverse of has disposition http://purl.obolibrary.org/obo/BSPO_0000120 in left side of http://purl.obolibrary.org/obo/BSPO_0000126 in lateral side of X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. http://purl.obolibrary.org/obo/BSPO_0000121 in right side of http://purl.obolibrary.org/obo/BSPO_0000126 in lateral side of X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. http://purl.obolibrary.org/obo/BSPO_0000126 in lateral side of http://purl.obolibrary.org/obo/BFO_0000050 part_of X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure http://purl.obolibrary.org/obo/BSPO_0001107 immediately deep to http://purl.obolibrary.org/obo/BSPO_0000107 deep to x immediately deep to y iff x deep_to y and x is contiguous with y. http://purl.obolibrary.org/obo/BSPO_0015014 immediately superficial to http://purl.obolibrary.org/obo/BSPO_0000108 superficial to x immediately superficial to y iff x superficial to y and x is contiguous with y. http://purl.obolibrary.org/obo/RO_0011002 regulates activity of http://purl.obolibrary.org/obo/RO_0002566 causally influences The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. http://purl.obolibrary.org/obo/RO_0002411 causally upstream of http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. http://purl.obolibrary.org/obo/RO_0002211 regulates http://purl.obolibrary.org/obo/RO_0002411 causally upstream of p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. http://purl.obolibrary.org/obo/RO_0002212 negatively regulates http://purl.obolibrary.org/obo/RO_0002211 regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. http://purl.obolibrary.org/obo/RO_0002213 positively regulates http://purl.obolibrary.org/obo/RO_0002211 regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. http://purl.obolibrary.org/obo/RO_0002180 has component http://purl.obolibrary.org/obo/BFO_0000051 has_part w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. http://purl.obolibrary.org/obo/RO_0002163 spatially disjoint from http://purl.obolibrary.org/obo/RO_0002323 mereotopologically related to A is spatially_disjoint_from B if and only if they have no parts in common http://purl.obolibrary.org/obo/RO_0002352 input of http://purl.obolibrary.org/obo/RO_0002328 functionally related to inverse of has input http://purl.obolibrary.org/obo/RO_0002203 develops into http://purl.obolibrary.org/obo/RO_0002387 has potential to develop into inverse of develops from http://purl.obolibrary.org/obo/RO_0002387 has potential to develop into http://purl.obolibrary.org/obo/RO_0002384 has developmental potential involving x has the potential to develop into y iff x develops into y or if x is capable of developing into y http://purl.obolibrary.org/obo/RO_0002023 directly negatively regulated by http://purl.obolibrary.org/obo/RO_0002022 directly regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. http://purl.obolibrary.org/obo/RO_0002024 directly positively regulated by http://purl.obolibrary.org/obo/RO_0002022 directly regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. http://purl.obolibrary.org/obo/RO_0012011 indirectly causally upstream of http://purl.obolibrary.org/obo/RO_0002411 causally upstream of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. http://purl.obolibrary.org/obo/RO_0012012 indirectly regulates http://purl.obolibrary.org/obo/RO_0012011 indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within http://purl.obolibrary.org/obo/RO_0002500 causal agent in process c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. http://purl.obolibrary.org/obo/RO_0002572 luminal space of http://purl.obolibrary.org/obo/RO_0002571 lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity http://purl.obolibrary.org/obo/RO_0004031 enables subfunction http://purl.obolibrary.org/obo/RO_0002328 functionally related to Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. http://purl.obolibrary.org/obo/RO_0004034 acts upstream of, positive effect http://purl.obolibrary.org/obo/RO_0004032 acts upstream of or within, positive effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive http://purl.obolibrary.org/obo/RO_0004035 acts upstream of, negative effect http://purl.obolibrary.org/obo/RO_0004033 acts upstream of or within, negative effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative http://purl.obolibrary.org/obo/RO_0002255 developmentally contributes to http://purl.obolibrary.org/obo/RO_0002385 has potential to developmentally contribute to inverse of has developmental contribution from http://purl.obolibrary.org/obo/RO_0002334 regulated by http://purl.obolibrary.org/obo/RO_0002427 causally downstream of or within inverse of regulates http://purl.obolibrary.org/obo/RO_0002335 negatively regulated by http://purl.obolibrary.org/obo/RO_0002334 regulated by inverse of negatively regulates http://purl.obolibrary.org/obo/RO_0002336 positively regulated by http://purl.obolibrary.org/obo/RO_0002334 regulated by inverse of positively regulates http://purl.obolibrary.org/obo/RO_0002385 has potential to developmentally contribute to http://purl.obolibrary.org/obo/RO_0002384 has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y http://purl.obolibrary.org/obo/RO_0002427 causally downstream of or within http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes inverse of causally upstream of or within http://purl.obolibrary.org/obo/RO_0002500 causal agent in process http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process A relationship between a material entity and a process where the material entity has some causal role that influences the process http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes http://purl.obolibrary.org/obo/RO_0002410 causally related to p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. http://purl.obolibrary.org/obo/RO_0002584 has part structure that is capable of http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. http://purl.obolibrary.org/obo/RO_0002596 capable of regulating http://purl.obolibrary.org/obo/RO_0002500 causal agent in process Holds between c and p if and only if c is capable of some activity a, and a regulates p. http://purl.obolibrary.org/obo/RO_0002597 capable of negatively regulating http://purl.obolibrary.org/obo/RO_0002596 capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. http://purl.obolibrary.org/obo/RO_0002598 capable of positively regulating http://purl.obolibrary.org/obo/RO_0002596 capable of regulating Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. http://purl.obolibrary.org/obo/RO_0002608 process has causal agent http://purl.obolibrary.org/obo/RO_0002410 causally related to Inverse of 'causal agent in process' http://purl.obolibrary.org/obo/RO_0002015 has positive regulatory component activity http://purl.obolibrary.org/obo/RO_0002013 has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. http://purl.obolibrary.org/obo/RO_0002013 has regulatory component activity http://purl.obolibrary.org/obo/RO_0002017 has component activity A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. http://purl.obolibrary.org/obo/RO_0002014 has negative regulatory component activity http://purl.obolibrary.org/obo/RO_0002013 has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. http://purl.obolibrary.org/obo/RO_0002428 involved in regulation of http://purl.obolibrary.org/obo/RO_0002431 involved in or involved in regulation of c involved in regulation of p if c is involved in some p' and p' regulates some p http://purl.obolibrary.org/obo/RO_0002429 involved in positive regulation of http://purl.obolibrary.org/obo/RO_0002428 involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p http://purl.obolibrary.org/obo/RO_0002430 involved in negative regulation of http://purl.obolibrary.org/obo/RO_0002428 involved in regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p http://purl.obolibrary.org/obo/RO_0002578 directly regulates http://purl.obolibrary.org/obo/RO_0002211 regulates p directly regulates q iff p is immediately causally upstream of q and p regulates q. http://purl.obolibrary.org/obo/RO_0002629 directly positively regulates http://purl.obolibrary.org/obo/RO_0002578 directly regulates p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. http://purl.obolibrary.org/obo/RO_0002630 directly negatively regulates http://purl.obolibrary.org/obo/RO_0002578 directly regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. http://purl.obolibrary.org/obo/RO_0002087 immediately preceded by http://purl.obolibrary.org/obo/BFO_0000062 preceded by starts_at_end_of http://purl.obolibrary.org/obo/RO_0002090 immediately precedes http://purl.obolibrary.org/obo/BFO_0000063 precedes meets http://purl.obolibrary.org/obo/RO_0002447 phosphorylates http://purl.obolibrary.org/obo/RO_0002436 molecularly interacts with An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. http://purl.obolibrary.org/obo/RO_0002405 immediately causally downstream of http://purl.obolibrary.org/obo/RO_0002404 causally downstream of http://purl.obolibrary.org/obo/RO_0002017 has component activity http://purl.obolibrary.org/obo/RO_0002018 has component process http://purl.obolibrary.org/obo/RO_0002559 causally influenced by http://purl.obolibrary.org/obo/RO_0002506 causal relation between entities http://purl.obolibrary.org/obo/RO_0002563 interaction relation helper property http://purl.obolibrary.org/obo/RO_0002464 helper property (not for use in curation) http://purl.obolibrary.org/obo/RO_0002564 molecular interaction relation helper property http://purl.obolibrary.org/obo/RO_0002563 interaction relation helper property http://purl.obolibrary.org/obo/RO_0002481 is kinase activity http://purl.obolibrary.org/obo/RO_0002564 molecular interaction relation helper property http://purl.obolibrary.org/obo/RO_0002086 ends after http://purl.obolibrary.org/obo/RO_0002222 temporally related to http://purl.obolibrary.org/obo/RO_0002092 happens during http://purl.obolibrary.org/obo/RO_0002093 ends during http://purl.obolibrary.org/obo/RO_0004033 acts upstream of or within, negative effect http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within http://purl.obolibrary.org/obo/RO_0004032 acts upstream of or within, positive effect http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within http://purl.obolibrary.org/obo/RO_0002022 directly regulated by http://purl.obolibrary.org/obo/RO_0002334 regulated by http://purl.obolibrary.org/obo/RO_0002506 causal relation between entities http://purl.obolibrary.org/obo/RO_0002410 causally related to http://purl.obolibrary.org/obo/RO_0004046 causally upstream of or within, negative effect http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within http://purl.obolibrary.org/obo/RO_0004047 causally upstream of or within, positive effect http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within http://purl.obolibrary.org/obo/RO_0000053 has characteristic is bearer of Inverse of characteristic_of http://purl.obolibrary.org/obo/RO_0000056 participates in participates_in a relation between a continuant and a process, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0000057 has participant has_participant a relation between a process and a continuant, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0001000 derives from derives_from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001001 derives into derives_into a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/BFO_0000066 occurs in unfolds_in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/RO_0002324 developmentally related to A relationship that holds between entities participating in some developmental process (GO:0032502) http://purl.obolibrary.org/obo/BFO_0000067 contains process [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/IAO_0000136 is about A (currently) primitive relation that relates an information artifact to an entity. http://purl.obolibrary.org/obo/RO_0017001 device utilizes material X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. http://purl.obolibrary.org/obo/RO_0003000 produces a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. http://purl.obolibrary.org/obo/RO_0003001 produced by a produced_by b iff some process that occurs_in b has_output a. http://purl.obolibrary.org/obo/RO_0002434 interacts with A relationship that holds between two entities in which the processes executed by the two entities are causally connected. http://purl.obolibrary.org/obo/BSPO_0001102 parallel to x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. http://purl.obolibrary.org/obo/BSPO_0000096 anterior to x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. http://purl.obolibrary.org/obo/BSPO_0000098 dorsal to x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). http://purl.obolibrary.org/obo/BSPO_0000099 posterior to x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. http://purl.obolibrary.org/obo/BSPO_0000102 ventral to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). http://purl.obolibrary.org/obo/BSPO_0000104 approximately perpendicular to Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. http://purl.obolibrary.org/obo/BSPO_0000107 deep to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. http://purl.obolibrary.org/obo/BSPO_0000108 superficial to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. http://purl.obolibrary.org/obo/BSPO_0000113 opposite to Direcly opposite to. i.e. on the opposite side through the axis. http://purl.obolibrary.org/obo/BSPO_0015005 orthogonal to crossing at right angles http://purl.obolibrary.org/obo/BSPO_0015006 passes through Intersects at two points. http://purl.obolibrary.org/obo/RO_0002323 mereotopologically related to A mereological relationship or a topological relationship http://purl.obolibrary.org/obo/RO_0002328 functionally related to A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. http://purl.obolibrary.org/obo/IAO_0000235 denoted by inverse of the relation 'denotes' http://purl.obolibrary.org/obo/RO_0002410 causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. http://purl.obolibrary.org/obo/RO_0002479 has part that occurs in p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. http://purl.obolibrary.org/obo/RO_0001018 contained in contained_in http://purl.obolibrary.org/obo/RO_0002464 helper property (not for use in curation) http://purl.obolibrary.org/obo/RO_0002487 relation between physical entity and a process or stage http://purl.obolibrary.org/obo/BSPO_0015001 finishes axis http://purl.obolibrary.org/obo/BSPO_0015007 starts axis http://purl.obolibrary.org/obo/BSPO_0015008 surface of http://purl.obolibrary.org/obo/RO_0002222 temporally related to http://purl.obolibrary.org/obo/RO_0002093 ends during http://purl.obolibrary.org/obo/RO_0002502 depends on http://purl.obolibrary.org/obo/RO_0001019 contains