XP:biological process xp self
From GO Public
cross-products within BP
Implmentation responsibility: Jennifer Deegan.
Progress notes: biological_process_xp_self_ProgressNotes
This is mostly temporal xps: definitions of terms based on a genus term and a larger containing process
This extends:
And should thus be non-redundant with them; you should see no xp defs involving the regulates link.
However, we do expect xps such as the following:
[Term] id: GO:0006933 ! negative regulation of cell adhesion involved in substrate-bound cell migration intersection_of: GO:0007162 ! negative regulation of cell adhesion intersection_of: part_of GO:0006929 ! substrate-bound cell migration
this is technically not a regulation xp: we can further expand the xp using the regulation xps to get
( (biological_regulation ^ regulates(cell_adhesion)) ^ part_of(substrate-bound cell migration) )
Contents |
[edit] Methods
Obol was used to generate the initial version of the file. Obol grammar: obol_biological_process_xp_self prolog grammar.
In contrast to many of the other XP files, an additional approach was used to seed potential xps defs: for each term, is_a and part_of pairs were tested to see if they were unique to that term. If unique, the links were used in the xp def. Note that this inevitably leads to "false positives" - necessary and sufficient conditions that are also satisfied by other terms. These were all examined by cjm, but some may have slipped through.
[edit] ontologies used
- GO (BP)
- RO
- ro_proposed
[edit] availability
[edit] Results
I have not submitted a tracker item here, because as this is a first pass many of the xps may be wrong. The strategy here is to first do a very cursory look through the list below to tell if there are systematic errors with the xp file:
"adaptation to pheromone during conjugation with cellular fusion" [GO:0000754] is_a "response to pheromone during conjugation with cellular fusion" [GO:0000749]
"adaptation to pheromone during conjugation without cellular fusion" [GO:0000760] is_a "response to pheromone during conjugation without cellular fusion" [GO:0000756]
"cellular morphogenesis during pheromone-induced unidirectional conjugation" [GO:0000764] is_a "cellular morphogenesis during unidirectional conjugation" [GO:0000763]
"adaptation to pheromone during pheromone-induced unidirectional conjugation" [GO:0000766] is_a "response to pheromone during pheromone-induced unidirectional conjugation" [GO:0000765]
"antral ovarian follicle growth" [GO:0001547] is_a "reproductive developmental process" [GO:0003006]
"oocyte maturation" [GO:0001556] is_a "reproductive cellular process" [GO:0048610]
"optic lobe placode development" [GO:0001748] is_a "embryonic eye morphogenesis" [GO:0048048]
"Mullerian duct regression" [GO:0001880] is_a "reproductive developmental process" [GO:0003006]
"embryonic placenta development" [GO:0001892] is_a "embryonic organ morphogenesis" [GO:0048562]
"embryonic placenta development" [GO:0001892] is_a "embryonic organ development" [GO:0048568]
"auditory receptor cell morphogenesis" [GO:0002093] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"gene conversion of immunoglobulin genes" [GO:0002206] is_a "gene conversion of immunoglobulin genes during immune response" [GO:0002207]
"alpha-beta T cell differentiation during immune response" [GO:0002293] is_a "alpha-beta T cell activation during immune response" [GO:0002287]
"gamma-delta T cell differentiation during immune response" [GO:0002303] is_a "gamma-delta T cell activation during immune response" [GO:0002290]
"gamma-delta T cell proliferation during immune response" [GO:0002311] is_a "gamma-delta T cell activation during immune response" [GO:0002290]
"immunoglobulin production" [GO:0002377] is_a "immunoglobulin production during immune response" [GO:0002381]
"immunoglobulin biosynthetic process" [GO:0002378] is_a "immunoglobulin biosynthetic process during immune response" [GO:0002379]
"basophil degranulation" [GO:0002561] is_a "basophil activation during immune response" [GO:0002276]
"spindle assembly involved in male meiosis" [GO:0007053] is_a "meiotic spindle organization and biogenesis" [GO:0000212]
"spindle assembly involved in female meiosis" [GO:0007056] is_a "meiotic spindle organization and biogenesis" [GO:0000212]
"pole cell development" [GO:0007277] is_a "reproductive cellular process" [GO:0048610]
"pole cell fate determination" [GO:0007278] is_a "reproductive cellular process" [GO:0048610]
"germ cell development" [GO:0007281] is_a "reproductive cellular process" [GO:0048610]
"oocyte construction" [GO:0007308] is_a "reproductive cellular process" [GO:0048610]
"egg activation" [GO:0007343] is_a "reproductive cellular process" [GO:0048610]
"gastrulation" [GO:0007369] is_a "embryonic morphogenesis" [GO:0048598]
"posterior midgut invagination" [GO:0007374] is_a "embryonic morphogenesis" [GO:0048598]
"germ-band extension" [GO:0007377] is_a "embryonic morphogenesis" [GO:0048598]
"germ-band shortening" [GO:0007390] is_a "embryonic morphogenesis" [GO:0048598]
"initiation of dorsal closure" [GO:0007392] is_a "embryonic morphogenesis" [GO:0048598]
"suture of dorsal opening" [GO:0007396] is_a "embryonic morphogenesis" [GO:0048598]
"anterior midgut (ectodermal) morphogenesis" [GO:0007441] is_a "embryonic anterior midgut (ectodermal) morphogenesis" [GO:0048615]
"donor selection" [GO:0007535] is_a "reproductive developmental process" [GO:0003006]
"donor selection" [GO:0007535] is_a "reproductive cellular process" [GO:0048610]
"sex determination, somatic-gonadal interaction" [GO:0007543] is_a "reproductive cellular process" [GO:0048610]
"embryo implantation" [GO:0007566] is_a "reproductive developmental process" [GO:0003006]
"mesodermal cell migration" [GO:0008078] is_a "cell migration involved in gastrulation" [GO:0042074]
"head involution" [GO:0008258] is_a "embryonic morphogenesis" [GO:0048598]
"embryonic development ending in seed dormancy" [GO:0009793] is_a "reproductive developmental process" [GO:0003006]
"pollen germination" [GO:0009846] is_a "reproductive cellular process" [GO:0048610]
"jasmonic acid and ethylene-dependent systemic resistance, jasmonic acid mediated signaling pathway" [GO:0009868] is_a "response to jasmonic acid stimulus during jasmonic acid and ethylene-dependent systemic resistance" [GO:0032260]
"longitudinal axis specification" [GO:0009942] is_a "embryonic axis specification" [GO:0000578]
"radial axis specification" [GO:0009945] is_a "embryonic axis specification" [GO:0000578]
"anastral spindle assembly involved in male meiosis" [GO:0009971] is_a "spindle assembly involved in male meiosis" [GO:0007053]
"seed dormancy" [GO:0010162] is_a "reproductive developmental process" [GO:0003006]
"seed coat development" [GO:0010214] is_a "reproductive developmental process" [GO:0003006]
"vegetative to reproductive phase transition" [GO:0010228] is_a "reproductive developmental process" [GO:0003006]
"maintenance of seed dormancy" [GO:0010231] is_a "reproductive developmental process" [GO:0003006]
"nectary development" [GO:0010254] is_a "reproductive developmental process" [GO:0003006]
"guard cell morphogenesis" [GO:0010442] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"primary neural tube formation" [GO:0014020] is_a "embryonic morphogenesis" [GO:0048598]
"secondary neural tube formation" [GO:0014021] is_a "embryonic morphogenesis" [GO:0048598]
"neural plate elongation" [GO:0014022] is_a "embryonic morphogenesis" [GO:0048598]
"somatic diversification of immunoglobulins" [GO:0016445] is_a "somatic diversification of immunoglobulins during immune response" [GO:0002208]
"somatic hypermutation of immunoglobulin genes" [GO:0016446] is_a "somatic hypermutation of immunoglobulin genes during immune response" [GO:0002205]
"neural fold bending" [GO:0021503] is_a "embryonic morphogenesis" [GO:0048598]
"inductive cell-cell signaling between paraxial mesoderm and motor neuron precursors" [GO:0021916] is_a "cell-cell signaling during cell fate commitment" [GO:0045168]
"initiation of neural tube closure" [GO:0021993] is_a "embryonic morphogenesis" [GO:0048598]
"progression of neural tube closure" [GO:0021994] is_a "embryonic morphogenesis" [GO:0048598]
"neuropore closure" [GO:0021995] is_a "embryonic morphogenesis" [GO:0048598]
"neural plate pattern formation" [GO:0021997] is_a "embryonic axis specification" [GO:0000578]
"peroxisomal membrane disassembly" [GO:0030398] is_a "autophagic membrane disassembly" [GO:0030399]
"sorocarp development" [GO:0030587] is_a "reproductive developmental process" [GO:0003006]
"aggregation involved in sorocarp development" [GO:0031152] is_a "reproductive developmental process" [GO:0003006]
"slug development during sorocarp development" [GO:0031153] is_a "reproductive developmental process" [GO:0003006]
"culmination during sorocarp development" [GO:0031154] is_a "reproductive developmental process" [GO:0003006]
"neurite development" [GO:0031175] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"sorocarp morphogenesis" [GO:0031288] is_a "reproductive developmental process" [GO:0003006]
"ascospore-type prospore formation" [GO:0031321] is_a "reproductive cellular process" [GO:0048610]
"somite rostral/caudal axis specification" [GO:0032525] is_a "embryonic axis specification" [GO:0000578]
"meiotic spindle checkpoint" [GO:0033316] is_a "meiotic cell cycle checkpoint" [GO:0033313]
"centrosomal and pronuclear rotation" [GO:0035047] is_a "reproductive developmental process" [GO:0003006]
"centrosomal and pronuclear rotation" [GO:0035047] is_a "reproductive cellular process" [GO:0048610]
"embryonic heart tube development" [GO:0035050] is_a "embryonic organ development" [GO:0048568]
"non-sensory hair organization and biogenesis" [GO:0035316] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"imaginal disc-derived wing hair outgrowth" [GO:0035318] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"imaginal disc-derived wing hair elongation" [GO:0035319] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"eye pigment metabolic process" [GO:0042441] is_a "pigment metabolic process during developmental pigmentation" [GO:0043324]
"ear morphogenesis" [GO:0042471] is_a "embryonic organ morphogenesis" [GO:0048562]
"inner ear morphogenesis" [GO:0042472] is_a "embryonic morphogenesis" [GO:0048598]
"outer ear morphogenesis" [GO:0042473] is_a "embryonic morphogenesis" [GO:0048598]
"middle ear morphogenesis" [GO:0042474] is_a "embryonic morphogenesis" [GO:0048598]
"embryonic digit morphogenesis" [GO:0042733] is_a "embryonic morphogenesis" [GO:0048598]
"mast cell degranulation" [GO:0043303] is_a "mast cell activation during immune response" [GO:0002279]
"eosinophil degranulation" [GO:0043308] is_a "eosinophil activation during immune response" [GO:0002278]
"neutrophil degranulation" [GO:0043312] is_a "neutrophil activation during immune response" [GO:0002283]
"cytotoxic T cell degranulation" [GO:0043316] is_a "T cell activation during immune response" [GO:0002286]
"natural killer cell degranulation" [GO:0043320] is_a "natural killer cell activation during immune response" [GO:0002323]
"homologous chromosome segregation" [GO:0045143] is_a "meiotic chromosome segregation" [GO:0045132]
"meiotic sister chromatid segregation" [GO:0045144] is_a "meiotic chromosome segregation" [GO:0045132]
"isotype switching" [GO:0045190] is_a "B cell activation during immune response" [GO:0002312]
"ocellus pigment metabolic process" [GO:0046158] is_a "pigment metabolic process during pigmentation" [GO:0043474]
"embryonic leg joint morphogenesis" [GO:0046591] is_a "embryonic morphogenesis" [GO:0048598]
"dorsal closure, amnioserosa morphology change" [GO:0046664] is_a "embryonic morphogenesis" [GO:0048598]
"embryonic eye morphogenesis" [GO:0048048] is_a "optic lobe placode development" [GO:0001748]
"sex-specific pigmentation" [GO:0048071] is_a "reproductive developmental process" [GO:0003006]
"germ-line cyst formation" [GO:0048134] is_a "reproductive cellular process" [GO:0048610]
"germ-line cyst encapsulation" [GO:0048138] is_a "reproductive developmental process" [GO:0003006]
"inflorescence morphogenesis" [GO:0048281] is_a "reproductive developmental process" [GO:0003006]
"immunoglobulin secretion" [GO:0048305] is_a "immunoglobulin secretion during immune response" [GO:0002380]
"seed morphogenesis" [GO:0048317] is_a "reproductive developmental process" [GO:0003006]
"mucilage biosynthetic process during seed coat development" [GO:0048354] is_a "mucilage metabolic process during seed coat development" [GO:0048359]
"floral whorl development" [GO:0048438] is_a "reproductive developmental process" [GO:0003006]
"recognition or rejection of self pollen" [GO:0048544] is_a "reproductive cellular process" [GO:0048610]
"embryonic gut morphogenesis" [GO:0048558] is_a "embryonic morphogenesis" [GO:0048598]
"oocyte morphogenesis" [GO:0048601] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"embryonic ectodermal gut development" [GO:0048611] is_a "embryonic morphogenesis" [GO:0048598]
"post-embryonic anterior midgut (ectodermal) morphogenesis" [GO:0048616] is_a "embryonic morphogenesis" [GO:0048598]
"embryonic foregut morphogenesis" [GO:0048617] is_a "embryonic morphogenesis" [GO:0048598]
"embryonic hindgut morphogenesis" [GO:0048619] is_a "embryonic morphogenesis" [GO:0048598]
"acquisition of desiccation tolerance" [GO:0048700] is_a "reproductive developmental process" [GO:0003006]
"embryonic cranial skeleton morphogenesis" [GO:0048701] is_a "embryonic morphogenesis" [GO:0048598]
"embryonic skeletal morphogenesis" [GO:0048704] is_a "embryonic organ morphogenesis" [GO:0048562]
"embryonic skeletal development" [GO:0048706] is_a "embryonic organ development" [GO:0048568]
"pigment biosynthetic process during pigment granule maturation" [GO:0048784] is_a "pigment metabolic process during developmental pigmentation" [GO:0043324]
"release of seed from dormancy" [GO:0048838] is_a "reproductive developmental process" [GO:0003006]
"behavioral response to nutrient" [GO:0051780] is_a "chemosensory behavior" [GO:0007635]
"astral spindle assembly involved in male meiosis" [GO:0055050] is_a "spindle assembly involved in male meiosis" [GO:0007053]
"Sertoli cell proliferation" [GO:0060011] is_a "reproductive cellular process" [GO:0048610]
"synaptic transmission involved in micturition" [GO:0060084] is_a "smooth muscle relaxation of the bladder outlet" [GO:0060085]
"smooth muscle relaxation of the bladder outlet" [GO:0060085] is_a "synaptic transmission involved in micturition" [GO:0060084]
"vestibular receptor cell morphogenesis" [GO:0060116] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"inner ear receptor stereocilium organization and biogenesis" [GO:0060122] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"re-entry into mitotic cell cycle after pheromone arrest" [GO:0000321] is_a "reproductive cellular process" [GO:0048610]
"meiotic DNA recombinase assembly" [GO:0000707] is_a "reproductive cellular process" [GO:0048610]
"meiotic DNA repair synthesis" [GO:0000711] is_a "premeiotic DNA synthesis" [GO:0006279]
"cell cycle arrest in response to pheromone" [GO:0000751] is_a "reproductive cellular process" [GO:0048610]
"agglutination during conjugation with cellular fusion" [GO:0000752] is_a "reproductive cellular process" [GO:0048610]
"cumulus cell differentiation" [GO:0001549] is_a "reproductive developmental process" [GO:0003006]
"cumulus cell differentiation" [GO:0001549] is_a "reproductive cellular process" [GO:0048610]
"oocyte growth" [GO:0001555] is_a "reproductive developmental process" [GO:0003006]
"oocyte growth" [GO:0001555] is_a "reproductive cellular process" [GO:0048610]
"oocyte maturation" [GO:0001556] is_a "reproductive developmental process" [GO:0003006]
"patterning of blood vessels" [GO:0001569] is_a "embryonic morphogenesis" [GO:0048598]
"acrosome formation" [GO:0001675] is_a "reproductive developmental process" [GO:0003006]
"inner cell mass cellular morphogenesis" [GO:0001828] is_a "embryonic morphogenesis" [GO:0048598]
"trophectodermal cellular morphogenesis" [GO:0001831] is_a "embryonic morphogenesis" [GO:0048598]
"membrane fusion during acrosome reaction" [GO:0002078] is_a "reproductive cellular process" [GO:0048610]
"auditory receptor cell morphogenesis" [GO:0002093] is_a "embryonic morphogenesis" [GO:0048598]
"chromatin silencing" [GO:0006342] is_a "establishment and/or maintenance of chromatin architecture during transcription" [GO:0034401]
"establishment of chromatin silencing" [GO:0006343] is_a "establishment and/or maintenance of chromatin architecture during transcription" [GO:0034401]
"pole cell formation" [GO:0007279] is_a "reproductive developmental process" [GO:0003006]
"pole cell formation" [GO:0007279] is_a "reproductive cellular process" [GO:0048610]
"cystoblast division" [GO:0007282] is_a "reproductive cellular process" [GO:0048610]
"spermatogonial cell division" [GO:0007284] is_a "reproductive cellular process" [GO:0048610]
"primary spermatocyte growth" [GO:0007285] is_a "reproductive developmental process" [GO:0003006]
"primary spermatocyte growth" [GO:0007285] is_a "reproductive cellular process" [GO:0048610]
"spermatid development" [GO:0007286] is_a "reproductive cellular process" [GO:0048610]
"sperm axoneme assembly" [GO:0007288] is_a "reproductive cellular process" [GO:0048610]
"spermatid nuclear differentiation" [GO:0007289] is_a "reproductive cellular process" [GO:0048610]
"spermatid nuclear elongation" [GO:0007290] is_a "reproductive cellular process" [GO:0048610]
"sperm individualization" [GO:0007291] is_a "reproductive developmental process" [GO:0003006]
"sperm individualization" [GO:0007291] is_a "reproductive cellular process" [GO:0048610]
"germarium-derived egg chamber formation" [GO:0007293] is_a "reproductive developmental process" [GO:0003006]
"germarium-derived oocyte fate determination" [GO:0007294] is_a "reproductive cellular process" [GO:0048610]
"growth of a germarium-derived egg chamber" [GO:0007295] is_a "reproductive developmental process" [GO:0003006]
"vitellogenesis" [GO:0007296] is_a "reproductive cellular process" [GO:0048610]
"ovarian follicle cell migration" [GO:0007297] is_a "reproductive cellular process" [GO:0048610]
"ovarian follicle cell adhesion" [GO:0007299] is_a "reproductive cellular process" [GO:0048610]
"nurse cell nucleus anchoring" [GO:0007302] is_a "reproductive cellular process" [GO:0048610]
"eggshell chorion formation" [GO:0007306] is_a "reproductive developmental process" [GO:0003006]
"oocyte axis determination" [GO:0007309] is_a "reproductive developmental process" [GO:0003006]
"oocyte dorsal/ventral axis determination" [GO:0007310] is_a "reproductive developmental process" [GO:0003006]
"oocyte anterior/posterior axis determination" [GO:0007314] is_a "reproductive developmental process" [GO:0003006]
"gonadal mesoderm development" [GO:0007506] is_a "reproductive developmental process" [GO:0003006]
"mating type switching" [GO:0007533] is_a "reproductive cellular process" [GO:0048610]
"dorsal/ventral axis determination, ovarian follicular epithelium" [GO:0008069] is_a "reproductive developmental process" [GO:0003006]
"dorsal/ventral axis determination, ovarian follicular epithelium" [GO:0008069] is_a "reproductive cellular process" [GO:0048610]
"mesodermal cell migration" [GO:0008078] is_a "cell motility involved in cell locomotion" [GO:0048870]
"ring canal formation, actin assembly" [GO:0008302] is_a "reproductive cellular process" [GO:0048610]
"germ cell migration" [GO:0008354] is_a "reproductive cellular process" [GO:0048610]
"pollen tube growth" [GO:0009860] is_a "reproductive developmental process" [GO:0003006]
"pollen tube growth" [GO:0009860] is_a "reproductive cellular process" [GO:0048610]
"pollen tube adhesion" [GO:0009865] is_a "reproductive cellular process" [GO:0048610]
"pollen adhesion" [GO:0009876] is_a "reproductive cellular process" [GO:0048610]
"longitudinal axis specification" [GO:0009942] is_a "reproductive developmental process" [GO:0003006]
"radial axis specification" [GO:0009945] is_a "reproductive developmental process" [GO:0003006]
"endosperm development" [GO:0009960] is_a "reproductive developmental process" [GO:0003006]
"oocyte differentiation" [GO:0009994] is_a "reproductive developmental process" [GO:0003006]
"oocyte differentiation" [GO:0009994] is_a "reproductive cellular process" [GO:0048610]
"zygote asymmetric cytokinesis in the embryo sac" [GO:0010069] is_a "reproductive cellular process" [GO:0048610]
"specification of floral organ identity" [GO:0010093] is_a "reproductive developmental process" [GO:0003006]
"synergid death" [GO:0010198] is_a "reproductive developmental process" [GO:0003006]
"synergid death" [GO:0010198] is_a "reproductive cellular process" [GO:0048610]
"floral organ abscission" [GO:0010227] is_a "reproductive developmental process" [GO:0003006]
"seed oilbody biogenesis" [GO:0010344] is_a "reproductive cellular process" [GO:0048610]
"inflorescence meristem growth" [GO:0010450] is_a "reproductive developmental process" [GO:0003006]
"floral meristem growth" [GO:0010451] is_a "reproductive developmental process" [GO:0003006]
"microsporocyte differentiation" [GO:0010480] is_a "reproductive developmental process" [GO:0003006]
"microsporocyte differentiation" [GO:0010480] is_a "reproductive cellular process" [GO:0048610]
"pronuclear envelope synthesis" [GO:0018985] is_a "reproductive cellular process" [GO:0048610]
"viral envelope fusion with host membrane" [GO:0019064] is_a "reproductive cellular process" [GO:0048610]
"virus assembly" [GO:0019068] is_a "reproductive cellular process" [GO:0048610]
"viral DNA genome packaging" [GO:0019073] is_a "reproductive cellular process" [GO:0048610]
"neural fold folding" [GO:0021505] is_a "embryonic morphogenesis" [GO:0048598]
"anterior neuropore closure" [GO:0021506] is_a "embryonic morphogenesis" [GO:0048598]
"posterior neuropore closure" [GO:0021507] is_a "embryonic morphogenesis" [GO:0048598]
"cell movement involved in somal translocation" [GO:0021805] is_a "cell motility involved in cell locomotion" [GO:0048870]
"initiation of movement involved in cerebral cortex radial glia guided migration" [GO:0021806] is_a "cell locomotion involved in cerebral cortex radial glia guided migration" [GO:0021814]
"cell locomotion involved in cerebral cortex radial glia guided migration" [GO:0021814] is_a "cell motility involved in cell locomotion" [GO:0048870]
"outward migration of deep nuclear neurons" [GO:0021947] is_a "cell motility involved in cell locomotion" [GO:0048870]
"inward migration of deep nuclear neurons" [GO:0021948] is_a "cell motility involved in cell locomotion" [GO:0048870]
"corticospinal neuron axon neuron guidance through the cerebral cortex" [GO:0021967] is_a "cell motility involved in cell locomotion" [GO:0048870]
"corticospinal neuron axon guidance through the internal capsule" [GO:0021968] is_a "cell motility involved in cell locomotion" [GO:0048870]
"corticospinal neuron axon guidance through the cerebral peduncle" [GO:0021969] is_a "cell motility involved in cell locomotion" [GO:0048870]
"corticospinal neuron axon guidance through the basilar pons" [GO:0021970] is_a "cell motility involved in cell locomotion" [GO:0048870]
"corticospinal neuron axon guidance through the medullary pyramid" [GO:0021971] is_a "cell motility involved in cell locomotion" [GO:0048870]
"corticospinal neuron axon guidance through the spinal cord" [GO:0021972] is_a "cell motility involved in cell locomotion" [GO:0048870]
"neural plate thickening" [GO:0021991] is_a "embryonic morphogenesis" [GO:0048598]
"lamina terminalis formation" [GO:0021996] is_a "embryonic morphogenesis" [GO:0048598]
"convergent extension involved in neural plate elongation" [GO:0022007] is_a "embryonic morphogenesis" [GO:0048598]
"menstrual cycle phase" [GO:0022601] is_a "reproductive developmental process" [GO:0003006]
"chorion-containing eggshell pattern formation" [GO:0030381] is_a "reproductive developmental process" [GO:0003006]
"ascospore wall assembly" [GO:0030476] is_a "reproductive cellular process" [GO:0048610]
"heteroduplex formation" [GO:0030491] is_a "reproductive cellular process" [GO:0048610]
"eggshell formation" [GO:0030703] is_a "reproductive developmental process" [GO:0003006]
"vitelline membrane formation" [GO:0030704] is_a "reproductive cellular process" [GO:0048610]
"ovarian follicle cell development" [GO:0030707] is_a "reproductive cellular process" [GO:0048610]
"anterior/posterior axis determination, follicular epithelium" [GO:0030714] is_a "reproductive developmental process" [GO:0003006]
"anterior/posterior axis determination, follicular epithelium" [GO:0030714] is_a "reproductive cellular process" [GO:0048610]
"karyosome formation" [GO:0030717] is_a "reproductive cellular process" [GO:0048610]
"ovarian fusome organization and biogenesis" [GO:0030723] is_a "reproductive cellular process" [GO:0048610]
"testicular fusome organization and biogenesis" [GO:0030724] is_a "reproductive cellular process" [GO:0048610]
"sorocarp stalk cell differentiation" [GO:0031149] is_a "reproductive developmental process" [GO:0003006]
"sorocarp stalk cell differentiation" [GO:0031149] is_a "reproductive cellular process" [GO:0048610]
"sorocarp stalk development" [GO:0031150] is_a "reproductive developmental process" [GO:0003006]
"ascospore-type prospore-specific spindle pole body modification" [GO:0031322] is_a "reproductive cellular process" [GO:0048610]
"mating projection biogenesis" [GO:0031382] is_a "cellular morphogenesis during conjugation with cellular fusion" [GO:0000753]
"signal transduction during conjugation with cellular fusion" [GO:0032005] is_a "reproductive cellular process" [GO:0048610]
"ascospore-type prospore membrane formation" [GO:0032120] is_a "reproductive cellular process" [GO:0048610]
"cell wall catabolic process during cytogamy" [GO:0032219] is_a "reproductive cellular process" [GO:0048610]
"otolith morphogenesis" [GO:0032474] is_a "embryonic morphogenesis" [GO:0048598]
"Leydig cell differentiation" [GO:0033327] is_a "reproductive developmental process" [GO:0003006]
"Leydig cell differentiation" [GO:0033327] is_a "reproductive cellular process" [GO:0048610]
"floor plate morphogenesis" [GO:0033505] is_a "embryonic morphogenesis" [GO:0048598]
"sexual sporulation" [GO:0034293] is_a "reproductive developmental process" [GO:0003006]
"sexual spore wall assembly" [GO:0034294] is_a "reproductive cellular process" [GO:0048610]
"sperm-egg recognition" [GO:0035036] is_a "reproductive cellular process" [GO:0048610]
"female pronucleus formation" [GO:0035038] is_a "reproductive cellular process" [GO:0048610]
"male pronucleus formation" [GO:0035039] is_a "reproductive cellular process" [GO:0048610]
"sperm plasma membrane disassembly" [GO:0035045] is_a "reproductive cellular process" [GO:0048610]
"sperm chromatin condensation" [GO:0035092] is_a "reproductive cellular process" [GO:0048610]
"behavioral response to nicotine" [GO:0035095] is_a "chemosensory behavior" [GO:0007635]
"genitalia morphogenesis" [GO:0035112] is_a "reproductive developmental process" [GO:0003006]
"embryonic medial fin morphogenesis" [GO:0035122] is_a "embryonic appendage morphogenesis" [GO:0035113]
"salt aversion" [GO:0035199] is_a "chemosensory behavior" [GO:0007635]
"germ cell attraction" [GO:0035232] is_a "reproductive behavior" [GO:0019098]
"germ cell repulsion" [GO:0035233] is_a "reproductive behavior" [GO:0019098]
"germ cell programmed cell death" [GO:0035234] is_a "reproductive developmental process" [GO:0003006]
"germ cell programmed cell death" [GO:0035234] is_a "reproductive cellular process" [GO:0048610]
"gonad morphogenesis" [GO:0035262] is_a "reproductive developmental process" [GO:0003006]
"germ-line stem cell division" [GO:0042078] is_a "reproductive cellular process" [GO:0048610]
"strand invasion" [GO:0042148] is_a "reproductive cellular process" [GO:0048610]
"progesterone secretion" [GO:0042701] is_a "reproductive cellular process" [GO:0048610]
"decidualization" [GO:0046697] is_a "reproductive developmental process" [GO:0003006]
"dorsal appendage formation" [GO:0046843] is_a "reproductive developmental process" [GO:0003006]
"micropyle formation" [GO:0046844] is_a "reproductive developmental process" [GO:0003006]
"spermatocyte division" [GO:0048137] is_a "reproductive cellular process" [GO:0048610]
"behavioral response to cocaine" [GO:0048148] is_a "chemosensory behavior" [GO:0007635]
"behavioral response to ethanol" [GO:0048149] is_a "chemosensory behavior" [GO:0007635]
"behavioral response to ether" [GO:0048150] is_a "chemosensory behavior" [GO:0007635]
"pollen sperm cell differentiation" [GO:0048235] is_a "reproductive developmental process" [GO:0003006]
"pollen sperm cell differentiation" [GO:0048235] is_a "reproductive cellular process" [GO:0048610]
"sperm capacitation" [GO:0048240] is_a "reproductive developmental process" [GO:0003006]
"sperm capacitation" [GO:0048240] is_a "reproductive cellular process" [GO:0048610]
"mucilage metabolic process during seed coat development" [GO:0048359] is_a "reproductive cellular process" [GO:0048610]
"floral organ development" [GO:0048437] is_a "reproductive developmental process" [GO:0003006]
"flower morphogenesis" [GO:0048439] is_a "reproductive developmental process" [GO:0003006]
"floral organ morphogenesis" [GO:0048444] is_a "reproductive developmental process" [GO:0003006]
"floral whorl morphogenesis" [GO:0048457] is_a "reproductive developmental process" [GO:0003006]
"floral whorl formation" [GO:0048458] is_a "reproductive developmental process" [GO:0003006]
"floral whorl structural organization" [GO:0048459] is_a "reproductive developmental process" [GO:0003006]
"flower formation" [GO:0048460] is_a "reproductive developmental process" [GO:0003006]
"flower structural organization" [GO:0048461] is_a "reproductive developmental process" [GO:0003006]
"style development" [GO:0048479] is_a "reproductive developmental process" [GO:0003006]
"stigma development" [GO:0048480] is_a "reproductive developmental process" [GO:0003006]
"ovule development" [GO:0048481] is_a "reproductive developmental process" [GO:0003006]
"ovule morphogenesis" [GO:0048482] is_a "reproductive developmental process" [GO:0003006]
"embryonic meristem development" [GO:0048508] is_a "reproductive developmental process" [GO:0003006]
"spermatid differentiation" [GO:0048515] is_a "reproductive developmental process" [GO:0003006]
"spermatid differentiation" [GO:0048515] is_a "reproductive cellular process" [GO:0048610]
"fruit morphogenesis" [GO:0048530] is_a "reproductive developmental process" [GO:0003006]
"oocyte fate commitment" [GO:0048600] is_a "reproductive cellular process" [GO:0048610]
"oocyte morphogenesis" [GO:0048601] is_a "reproductive developmental process" [GO:0003006]
"oocyte morphogenesis" [GO:0048601] is_a "reproductive cellular process" [GO:0048610]
"embryonic ectodermal gut development" [GO:0048611] is_a "embryonic gut development" [GO:0048566]
"embryonic ectodermal gut morphogenesis" [GO:0048613] is_a "embryonic gut morphogenesis" [GO:0048558]
"embryonic ectodermal gut morphogenesis" [GO:0048613] is_a "embryonic ectodermal gut development" [GO:0048611]
"anther development" [GO:0048653] is_a "reproductive developmental process" [GO:0003006]
"tapetal layer morphogenesis" [GO:0048655] is_a "reproductive developmental process" [GO:0003006]
"tapetal layer formation" [GO:0048656] is_a "reproductive developmental process" [GO:0003006]
"tapetal layer development" [GO:0048658] is_a "reproductive developmental process" [GO:0003006]
"embryonic neurocranium morphogenesis" [GO:0048702] is_a "embryonic morphogenesis" [GO:0048598]
"embryonic viscerocranium morphogenesis" [GO:0048703] is_a "embryonic morphogenesis" [GO:0048598]
"semicircular canal morphogenesis" [GO:0048752] is_a "embryonic morphogenesis" [GO:0048598]
"root hair initiation" [GO:0048766] is_a "cellular morphogenesis during differentiation" [GO:0000904]
"genitalia development" [GO:0048806] is_a "reproductive developmental process" [GO:0003006]
"cotyledon morphogenesis" [GO:0048826] is_a "reproductive developmental process" [GO:0003006]
"specification of floral organ number" [GO:0048833] is_a "reproductive developmental process" [GO:0003006]
"diapedesis" [GO:0050904] is_a "cell motility involved in cell locomotion" [GO:0048870]
"generative cell mitosis" [GO:0055047] is_a "reproductive cellular process" [GO:0048610]
"invagination involved in gastrulation with mouth forming second" [GO:0055109] is_a "embryonic morphogenesis" [GO:0048598]
"involution involved in gastrulation with mouth forming second" [GO:0055110] is_a "embryonic morphogenesis" [GO:0048598]
"epiboly involved in gastrulation with mouth forming second" [GO:0055113] is_a "embryonic morphogenesis" [GO:0048598]
"reproductive diapause" [GO:0055116] is_a "reproductive developmental process" [GO:0003006]
"Sertoli cell differentiation" [GO:0060008] is_a "reproductive developmental process" [GO:0003006]
"Sertoli cell differentiation" [GO:0060008] is_a "reproductive cellular process" [GO:0048610]
"Sertoli cell development" [GO:0060009] is_a "reproductive cellular process" [GO:0048610]
"Sertoli cell fate commitment" [GO:0060010] is_a "reproductive cellular process" [GO:0048610]
"convergent extension involved in gastrulation" [GO:0060027] is_a "embryonic morphogenesis" [GO:0048598]
"vestibular receptor cell morphogenesis" [GO:0060116] is_a "embryonic morphogenesis" [GO:0048598]
"syncytium formation by plasma membrane fusion of virally targeted cells" [GO:0060140] is_a "reproductive cellular process" [GO:0048610]
"cloacal septation" [GO:0060197] is_a "digestive tract morphogenesis" [GO:0048546]
"G1/S-specific transcription in mitotic cell cycle" [GO:0000083] is_a "regulation of transcription from RNA polymerase II promoter, mitotic" [GO:0046021]
"G1-specific transcription in mitotic cell cycle" [GO:0000114] is_a "regulation of transcription from RNA polymerase II promoter, mitotic" [GO:0046021]
"S-phase-specific transcription in mitotic cell cycle" [GO:0000115] is_a "regulation of transcription from RNA polymerase II promoter, mitotic" [GO:0046021]
"G2-specific transcription in mitotic cell cycle" [GO:0000116] is_a "regulation of transcription from RNA polymerase II promoter, mitotic" [GO:0046021]
"G2/M-specific transcription in mitotic cell cycle" [GO:0000117] is_a "regulation of transcription from RNA polymerase II promoter, mitotic" [GO:0046021]
"gene conversion at mating-type locus, DNA double-strand break formation" [GO:0000728] is_a "reproductive cellular process" [GO:0048610]
"gene conversion at mating-type locus, DNA repair synthesis" [GO:0000734] is_a "reproductive cellular process" [GO:0048610]
"removal of nonhomologous ends" [GO:0000735] is_a "reproductive cellular process" [GO:0048610]
"karyogamy during conjugation with cellular fusion" [GO:0000742] is_a "reproductive cellular process" [GO:0048610]
"nuclear migration during conjugation with cellular fusion" [GO:0000743] is_a "reproductive cellular process" [GO:0048610]
"cellular morphogenesis during conjugation with cellular fusion" [GO:0000753] is_a "reproductive developmental process" [GO:0003006]
"cellular morphogenesis during conjugation with cellular fusion" [GO:0000753] is_a "reproductive cellular process" [GO:0048610]
"ovarian follicle atresia" [GO:0001552] is_a "reproductive developmental process" [GO:0003006]
"ovarian follicle atresia" [GO:0001552] is_a "reproductive cellular process" [GO:0048610]
"acrosome matrix dispersal" [GO:0002077] is_a "reproductive cellular process" [GO:0048610]
"positive regulation of transcription on exit from mitosis" [GO:0007072] is_a "regulation of transcription, mitotic" [GO:0045896]
"Nebenkern formation" [GO:0007287] is_a "reproductive cellular process" [GO:0048610]
"ovarian ring canal formation" [GO:0007301] is_a "reproductive cellular process" [GO:0048610]
"eggshell chorion gene amplification" [GO:0007307] is_a "reproductive cellular process" [GO:0048610]
"pole plasm assembly" [GO:0007315] is_a "reproductive cellular process" [GO:0048610]
"fusion of sperm to egg plasma membrane" [GO:0007342] is_a "reproductive cellular process" [GO:0048610]
"pronuclear fusion" [GO:0007344] is_a "reproductive cellular process" [GO:0048610]
"gene conversion at mating-type locus" [GO:0007534] is_a "reproductive cellular process" [GO:0048610]
"oocyte microtubule cytoskeleton polarization" [GO:0008103] is_a "reproductive cellular process" [GO:0048610]
"ovarian ring canal stabilization" [GO:0008335] is_a "reproductive cellular process" [GO:0048610]
"cell wall modification during ripening" [GO:0009829] is_a "reproductive cellular process" [GO:0048610]
"pollen tube guidance" [GO:0010183] is_a "reproductive behavior" [GO:0019098]
"tapetal cell fate specification" [GO:0010234] is_a "reproductive cellular process" [GO:0048610]
"oocyte microtubule cytoskeleton organization" [GO:0016325] is_a "reproductive cellular process" [GO:0048610]
"provirus integration" [GO:0019047] is_a "reproductive cellular process" [GO:0048610]
"receptor mediated endocytosis of virus by host" [GO:0019065] is_a "reproductive cellular process" [GO:0048610]
"viral protein processing" [GO:0019082] is_a "reproductive cellular process" [GO:0048610]
"viral transcription" [GO:0019083] is_a "reproductive cellular process" [GO:0048610]
"midbrain-hindbrain boundary morphogenesis" [GO:0021555] is_a "embryonic morphogenesis" [GO:0048598]
"chemorepulsion of branchiomotor neuron axon in neural tube" [GO:0021787] is_a "cell motility involved in cell locomotion" [GO:0048870]
"chemoattraction of branchiomotor neuron axon in neural tube" [GO:0021788] is_a "cell motility involved in cell locomotion" [GO:0048870]
"chemorepulsion of branchiomotor axon in branchial arch mesenchyme" [GO:0021790] is_a "cell motility involved in cell locomotion" [GO:0048870]
"chemoattraction of branchiomotor neuron axon in branchial arch mesenchyme" [GO:0021791] is_a "cell motility involved in cell locomotion" [GO:0048870]
"ovarian follicle cell stalk formation" [GO:0030713] is_a "reproductive developmental process" [GO:0003006]
"ovarian follicle cell stalk formation" [GO:0030713] is_a "reproductive cellular process" [GO:0048610]
"polar granule organization and biogenesis" [GO:0030719] is_a "reproductive cellular process" [GO:0048610]
"testicular ring canal formation" [GO:0030726] is_a "reproductive cellular process" [GO:0048610]
"embryonic camera-type eye development" [GO:0031076] is_a "embryonic organ development" [GO:0048568]
"gene conversion at mating-type locus, DNA double-strand break processing" [GO:0031292] is_a "reproductive cellular process" [GO:0048610]
"plasma membrane fusion during cytogamy" [GO:0032220] is_a "reproductive cellular process" [GO:0048610]
"ascospore wall chitin biosynthetic process" [GO:0034217] is_a "reproductive cellular process" [GO:0048610]
"actinomycete-type spore formation" [GO:0034304] is_a "reproductive developmental process" [GO:0003006]
"sperm entry" [GO:0035037] is_a "reproductive cellular process" [GO:0048610]
"sperm nuclear envelope removal" [GO:0035040] is_a "reproductive cellular process" [GO:0048610]
"sperm chromatin decondensation" [GO:0035041] is_a "reproductive cellular process" [GO:0048610]
"sperm aster formation" [GO:0035044] is_a "reproductive cellular process" [GO:0048610]
"follicle-stimulating hormone signaling pathway" [GO:0042699] is_a "reproductive cellular process" [GO:0048610]
"DNA methylation during gametogenesis" [GO:0043046] is_a "reproductive cellular process" [GO:0048610]
"nurse cell apoptosis" [GO:0045476] is_a "reproductive developmental process" [GO:0003006]
"nurse cell apoptosis" [GO:0045476] is_a "reproductive cellular process" [GO:0048610]
"viral DNA repair" [GO:0046787] is_a "reproductive cellular process" [GO:0048610]
"establishment of floral organ orientation" [GO:0048559] is_a "reproductive developmental process" [GO:0003006]
"tapetal cell differentiation" [GO:0048657] is_a "reproductive developmental process" [GO:0003006]
"tapetal cell differentiation" [GO:0048657] is_a "reproductive cellular process" [GO:0048610]
"oocyte nucleus localization during oocyte axis determination" [GO:0051663] is_a "reproductive cellular process" [GO:0048610]
"auditory receptor cell stereocilium organization and biogenesis" [GO:0060088] is_a "embryonic morphogenesis" [GO:0048598]
"vestibular receptor cell stereocilium organization and biogenesis" [GO:0060121] is_a "embryonic morphogenesis" [GO:0048598]
"Malpighian tubule morphogenesis" [GO:0007443] is_a "embryonic digestive tract morphogenesis" [GO:0048557]
"fertilization, exchange of chromosomal proteins" [GO:0035042] is_a "reproductive cellular process" [GO:0048610]
"spermatogenesis, exchange of chromosomal proteins" [GO:0035093] is_a "reproductive cellular process" [GO:0048610]
"mitotic sister chromatid segregation" [GO:0000070] is_a "chromosome segregation" [GO:0007059]
"double-strand break repair via single-strand annealing, removal of nonhomologous ends" [GO:0000736] is_a "removal of nonhomologous ends" [GO:0000735]
"feeding behavior" [GO:0007631] is_a "response to food" [GO:0032094]
"induction of phytoalexin biosynthetic process" [GO:0009689] is_a "induction" [GO:0031128]
"induction of conjugation with cellular fusion" [GO:0010514] is_a "induction" [GO:0031128]
"induction of programmed cell death" [GO:0012502] is_a "induction" [GO:0031128]
"midbrain-hindbrain boundary maturation during brain development" [GO:0022004] is_a "midbrain-hindbrain boundary maturation" [GO:0021732]
"midbrain-hindbrain boundary maturation during neural plate development" [GO:0022005] is_a "midbrain-hindbrain boundary maturation" [GO:0021732]
"embryonic camera-type eye development" [GO:0031076] is_a "camera-type eye development" [GO:0043010]
"mitochondrial fragmentation during apoptosis" [GO:0043653] is_a "mitochondrial fission" [GO:0000266]
"digestive tract morphogenesis" [GO:0048546] is_a "tube morphogenesis" [GO:0035239]
"embryonic gut morphogenesis" [GO:0048558] is_a "gut morphogenesis" [GO:0048547]
"embryonic camera-type eye morphogenesis" [GO:0048596] is_a "camera-type eye morphogenesis" [GO:0048593]
"embryonic ectodermal gut development" [GO:0048611] is_a "ectodermal gut development" [GO:0007439]
"embryonic ectodermal gut morphogenesis" [GO:0048613] is_a "ectodermal gut morphogenesis" [GO:0048567]
"embryonic anterior midgut (ectodermal) morphogenesis" [GO:0048615] is_a "anterior midgut (ectodermal) morphogenesis" [GO:0007441]
"embryonic foregut morphogenesis" [GO:0048617] is_a "foregut morphogenesis" [GO:0007440]
"embryonic hindgut morphogenesis" [GO:0048619] is_a "hindgut morphogenesis" [GO:0007442]
"circadian sleep/wake cycle, sleep" [GO:0050802] is_a "sleep" [GO:0030431]
"induction of negative chemotaxis" [GO:0050929] is_a "induction" [GO:0031128]
"induction of positive chemotaxis" [GO:0050930] is_a "induction" [GO:0031128]
"negative regulation by symbiont of entry into host cell via phagocytosis" [GO:0052067] is_a negative_regulation_by_symbiont_of_entry_into_host_cell
"embryonic retina morphogenesis in camera-type eye" [GO:0060059] is_a "retina morphogenesis in camera-type eye" [GO:0060042]
meiotic_transcription is_a "transcription" [GO:0006350]
Some of these may seem unusual; let's analyze one:
- "neural plate elongation" [GO:0014022] is_a "embryonic morphogenesis" [GO:0048598]
The full obol explanation is as follows:
"neural plate elongation" [GO:0014022] is_a "embryonic morphogenesis" [GO:0048598]
because of rule: genus_differentia :
"embryonic morphogenesis" [GO:0048598] is defined as {
a "anatomical structure morphogenesis" [GO:0009653] that
part_of "embryonic development" [GO:0009790] } ,
and it is the case that
"neural plate elongation" [GO:0014022] is_a "anatomical structure morphogenesis" [GO:0009653]
and
"neural plate elongation" [GO:0014022] part_of "embryonic development" [GO:0009790]
Which isn't exactly normal english.
Loading the xps into OE, we can ask for an explanation here (implied links are blue dashed lines):
It's still not exactly clear...
Here is my explanation:
- embryonic morphogenesis = any morphogenesis THAT is part_of embryonic development
- neural plate elongation is part_of embryonic development (by transitivity - can be seen in the graph above)
- neural plate elongation is_a anatomical structure morphogenesis (this is asserted in the ontology by editors)
[edit] Problems
[edit] Mitosis etc
obol parses 'mitotic spindle elongation' as
- spindle elongation THAT part_of mitosis
i.e.
[Term] id: GO:0000022 ! mitotic spindle elongation intersection_of: GO:0051231 ! spindle elongation intersection_of: part_of GO:0007067 ! mitosis
Perhaps these should be manually fixed to
- spindle elongation THAT part_of mitotic cell cycle
I have to confess I find this part of the ontology a bit confusing
[edit] part_of vs during / involved in
Obol treats the phrase "X during Y" as "X that part_of Y"
part_of is actually stronger than during. If we change these part_ofs to during relations in the xp file we will get less predicted is_a links
