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Changes to GO for alignment with cell ontology #2481

Closed gocentral closed 9 years ago

gocentral commented 19 years ago

* Action for CL

** Action for GO

missing extrathymic T-cell missing thymic T-cell missing negative extrathymic T-cell missing negative thymic T-cell missing positive extrathymic T-cell missing positive thymic T-cell ... no change to CL/GO needed; not a cell type but a cell location X-Sender: adiehl@popmgi.informatics.jax.org Date: Wed, 20 Apr 2005 12:39:21 -0400 # missing edge cell .. no action parse problem missing thymocyte .. no change to CL; GO in process of obsoleting/merging this term X-Sender: adiehl@popmgi.informatics.jax.org Date: Wed, 20 Apr 2005 12:39:21 -0400 # missing natural killer cell *.. is in CL. CL to add 'NK T-cell' & 'NK T cell' & 'NK T lymphocyte' as
synonyms. missing NK T-cell .. see above X-Sender: adiehl@popmgi.informatics.jax.org Date: Wed, 20 Apr 2005 12:39:21 -0400 # missing B-1 B-cell missing T-helper 1 cell missing T-helper 2 cell missing T-helper cell missing activated T-cell missing alpha-beta T-cell missing helper cell missing cytotoxic T-cell missing gamma-delta T-cell missing killer cell missing regulatory T-cell

CL to change all 'B_cell' 'T_cell' > 'B cell' 'T cell' with 'B-cell', 'B lymphocyte' as synonmyms. CL to change 'helper T cell' > 'T-helper cell' with former as synonym. *GO also to change 'B-cell' etc > 'B cell' etc with 'B cell', 'B lymphocyte' etc as synonyms. CL will not add terms above until Alex reports back. #

  1. Is the GO usage of 'hemocyte' arthropod specific ? In this case GO needs to change 'hemocyte differentiation (sensu Arthropoda)' by removing the sensu. *CL will change 'hemocyte' and 'prohemocyte' to ditto (sensu Arthropoda' X-Sender: adiehl@popmgi.informatics.jax.org Date: Wed, 20 Apr 2005 12:39:21 -0400 # missing azurophil .. not a cell type but a class of granule; parse error # GO has already changed 'neuron cell differentiation' > 'neuron differentiation' From: J Clark <jclark@ebi.ac.uk> Date: Mon, 18 Apr 2005 17:32:25 +0100 # basophil cell hemocyte cell neuroblast cell neuron cell oocyte cell spermatid cell spermatocyte cell synergid cell trichome cell missing cystoblast cell **GO to remove 'cell' from all of these. Note that 'egg cell' has been kept because that is plant useage. CL will keep 'egg cell' with the same meaning. From: J Clark <jclark@ebi.ac.uk> Date: Wed, 20 Apr 2005 15:47:29 +0100 #
  2. CL uses 'photoreceptor cell'; GO uses 'photoreceptor'. Are these the same? We need to normalize. Suggestions ? Same is true of GO's 'mechanoreceptor' and CL's 'mechanoreceptor cell'. CL should probably add R1..R8 as isa of 'eye photoreceptor cell' .. photorecptor and photoreceptor cell are not the same thing. The 'receptor' can be a single cell or the entire stucture (the eye is a photoreceptor, so are its rods and cones); ditto mechanoreceptor. CL no change except: GO: ADD 'eye photoreceptor cell ; CL:NEW' as isa 'photoreceptor cell' GO: ADD 'non-eye photoreceptor cell' non-eye photoreceptor cell #
  3. ADD 'male gametophyte sperm cell ; CL:NEW' as isa of 'sperm cell (sensu Viridiplantae' Sue argues that this is redundant: 'We feel that this is somewhat redundant since all Viridiplantae sperm cells come from the gametophyte.' Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rhee@acoma.Stanford.EDU> If so it is presumably redundant in GO: GO:0048235 : male gametophyte sperm cell GO to act # missing pollen not a cell but an organism (male gametophyte) Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rhee@acoma.Stanford.EDU> .. no action # These are Sue's comments Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rhee@acoma.Stanford.EDU> ... which indicate that a change to GO, rather than CL, is required: missing abaxial cell This is too vague a concept as a cell type and should not be included in CL. missing gametophyte central cell not necessary. female gametophyte central cell is sufficient. i believe that hermaphrodite gametophyte does not make a central cell. Also if 'central cell' is not used in other systems, the adjective 'female gametophyte' may not be necessary as part of the term name. missing gametophyte egg cell i don't think we need to make a distinction between gametophyte egg cell and female gametophyte egg cell. missing gametophyte sperm cell not necessary. we could add it as a synonym of sperm cell (sensu Viridiplantae) missing male gametophyte sperm cell not necessary. # missing primary endosperm perhaps endosperm cell might be needed. will look into this further and update the ontology. Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rhee@acoma.Stanford.EDU> CL to add # missing primary cell this probably comes from 'primary cell wall' and doesn't need to be added as a cell type. missing secondary cell this comes from 'secondary cell wall' and doesn't need to be added as a cell type. Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rhee@acoma.Stanford.EDU> .. no action parse problems # missing pollen germ cell this is not necessary as it's the same as male gametophyte sperm cell. also it is not a very good synonym. CL to make synonym GO is this then needed ?? Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rhee@acoma.Stanford.EDU> # CL. ADD as develops_from 'granulosa_cell': cumulus cell ; CL:NEW stratum granulosum cell ; CL:NEW with 'corona radiata cell ; CL:NEW' as being an isa cumulus cell CL. MAKE 'osteoclast' and 'macrophage' both isa's of 'monocyte' CL. change 'spermatozoan' to 'sperm' CL. ADD parent 'cardioblast ; CL:NEW' for 'cardioblast (sensu Arthropoda) CL. CORRECT spelling 'sperm cel' (synonym of CL:0000019). CL. REMOVE all and replaced by spaces. CL. CHANGE default-namespace: to 'cell' from 'cell_ontology'. CL. CHANGE 'epithelial cell of trachea' to 'tracheal epithelial cell' CL: make 'trichome' also an isa of 'hair cell' CL to addroot epidermal cell CL. CHANGE: 'blood platelet' > 'platelet' CL. ADD 'retinal cone cell ; CL:NEW' as isa 'cone cell' CL. ADD 'fusimotor neuron' is_a 'motor neuron' def: A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons. PMID:15582775 CL. ADD as isa child of 'crystal cell': embryonic crystal cell lymph gland crystal cell CL: add 'cystoblast' as child of 'germ cell'; make 'nurse cell' a developsfrom child CL: add 'somatic stem cell' as child of 'stem cell' CL. ADD new cell type: heterocyst, isa 'prokaryotic cell'; isa 'nitrogen fixing cell ; CL:NEW' definition: A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions. chlamydospore, isa a 'fungal cell'; isa 'asexual spore' definition: An asexual 1-celled spore (primarily for perennation, not dissemination) originating endogenously and singly within part of a pre-existing cell, by the contraction of the protoplast and possessing an inner secondary and oftened thickened hyaline or brown wall, usually impregnated with hydrophobic material. definition_reference: ISBN:085199377X CL to change 'leukocyte cell' > 'leukocyte' CL: correct spelling of 'iridiophore' to 'iridophore' CL: add 'primary pigment cell' 'secondary pigment cell' 'tertiary pigment cell'as childs of 'visual pigment cell (sensu Nematoda ..' CL: add 'cone cell (sensu Endoptyeygota)' as child of 'crystallin accumulating cell' with children 'posterior, anterior, polar & equatorial cone cell (sens E)' CL: add 'leading edge cell' as child of 'epithelial cell' with defn: 'A cell at the front of a migrating epithelial sheet.' CL: add 'urothelial cell' as child of 'epithelial cell' with defn: 'A cell of a layer of transitional epithelium in the wall of the bladder, ureter, and renal pelvis, external to the lamina propria'. CL: Add 'ameboid cell' as a child of ; make 'chemotactic ameoba' a child of it. defn: 'A cell that migrates by extension and retraction of a pseudopodium.' # GO to change 'tracheal cell ' to 'tracheal epithelial cell ' GO to change 'ovarian cumulus cell differentiation' to 'cumulus cell differentiation' GO to change 'auditory hair cell' to 'auditory receptor cell' GO to change 'branch cell fate determination (sensu Insecta) -> branched_duct_epithelialcell fate determination (sensu Insecta)' GO change 'glia cell' to 'glial cell'. GO change 'border cell' to 'border follicle cell'. GO. change 'leukocyte cell' to 'leukocyte'. GO: change 'mesoderm cell' to 'mesodermal cell' GO: change 'endoderm cell' to 'endodermal cell' GO: change 'neuronal cell' to 'neuron' **GO; add neuroblast(sensu_Nematoda_andProtostomia), neuroblast(sensuVertebrata) as childs of neuroblast [cell] * terms **GO; add erythrocyte(sensuMammalia), erythrocyte(sensu_non-Mammalia) as childs of of erythrocyte * terms GO add epidermalcell(sensu_Insecta) as childs of epidermal cell terms ? GO: ditto glial cell (sensu Nematoda and Protostomia) as childs of glial cell
    • terms ? *GO: ditto pigment cell (sensu Nematoda and Protostomia), pigment cell (sensu Vertebrata) as childs of pigment cell terms ? GO: male 'iridophore differentiation' and 'xanthophore differentiation' childs of 'melanocyte differentiation', not sibs GO: to change 'apidocyte' to 'fat cell' .. JB argued that 'apidocyte' as not understood by vertebrates. CL uses 'fat cell' with 'apidocyte' as a syn. #
  4. GO uses 'striated muscle cell'; CL has only 'obliquely striated muscle cell'. Is there any other type of striated muscle cell ? If so CL should change.

Delivery-date: Fri, 22 Apr 2005 10:05:07 +0100 From: Jonathan Bard <jbard@staffmail.ed.ac.uk> Striated muscle comes in two flavours - normal (default, longitudinal striations) and obliquely striated - a c elegans speciality (I suppose it is seen in other nematodes and such organisms)# CL: add 'striated muscle cell' as parent of 'obliquely striated muscle cell # missing embryonic crystal cell missing embryonic hemocyte missing embryonic plasmatocyte missing lymph gland crystal cell missing lymph gland hemocyte missing lymph gland plasmatocyte CL: add these terms as there is, indeed, two such pops in flies # Outstanding terms missing from CL. Any helpers ?

missing aortic cell (sensu Insecta) missing autophagic cell missing blood cell missing early stripe melanocyte missing gland cell missing inner cell mass cell missing larval midgut cell missing late stripe melanocyte missing stripe melanocyte missing mass cell missing mystery cell fate missing organ precursor cell missing precursor cell missing sensory organ precursor cell

missing polarized epithelial cell ... is there such a thing as an unpolarized epithelial cell ??

These all have similar constyct '<place> cell'

missing axial mesoderm cell missing lateral mesoderm cell missing intermediate mesoderm cell missing paraxial mesoderm cell missing salivary gland cell missing tracheal cell missing trophectoderm cell missing retinal cell missing heart proper cell missing cardiac cell missing midgut cell

#

Reported by: jl242

Original Ticket: "geneontology/ontology-requests/2488":https://sourceforge.net/p/geneontology/ontology-requests/2488

gocentral commented 19 years ago

Logged In: YES user_id=451873

Implemented the following in GO (not yet finished):

Removed 'cell' from all of these:

basophil cell hemocyte cell neuroblast cell neuron cell neuronal cell oocyte cell spermatid cell spermatocyte cell synergid cell trichome cell cystoblast cell

Added old string as synonym.

These:

GO: ADD 'eye photoreceptor cell ; CL:NEW' as isa 'photoreceptor cell' GO: ADD 'non-eye photoreceptor cell' non-eye photoreceptor cell

I think is action for CL not GO (should read CL: not GO:)?

Changed name of 'male gametophyte sperm cell differentiation ; GO:0048235' -> 'sperm cell differentiation (sensu Magnoliophyta)'

Changed name of 'pollen germ cell nucleus ; GO:0043075' -> 'sperm cell nucleus (sensu Magnoliophyta)'

Changed 'tracheal cell ' -> 'tracheal epithelial cell ' Changed ' ovarian cumulus cell ' -> ' cumulus cell ' Changed 'auditory hair cell ' -> 'auditory receptor cell ' Changed 'branch cell fate determination (sensu Insecta) ' -> 'branched duct epithelial cell fate determination (sensu Insecta) ' Changed 'glia cell ' -> 'glial cell ' Changed ' border cell ' -> ' border follicle cell ' Changed 'leukocyte cell' -> 'leukocyte' Changed 'mesoderm cell' -> 'mesodermal cell' Changed 'endoderm cell' -> 'endodermal cell'

Added new terms:

establishment and/or maintenance of neuroblast polarity (sensu Nematoda and Protostomia) ; GO:0043339 establishment of neuroblast polarity (sensu Nematoda and Protostomia) ; GO:0043340 maintenance of neuroblast polarity (sensu Nematoda and Protostomia) ; GO:0043341 establishment and/or maintenance of neuroblast polarity (sensu_Vertebrata) ; GO:0043342 establishment of neuroblast polarity (sensu_Vertebrata) ; GO:0043343 maintenance of neuroblast polarity (sensu_Vertebrata) ; GO:0043344 neuroblast division (sensu Vertebrata) ; GO:0043345 neuroblast division (sensu Nematoda and Protostomia) ; GO:0043346 neuroblast fate determination (sensu Nematoda and Protostomia) ; GO:0043347 neuroblast fate determination (sensu Vertebrata) ; GO:0043348 neuroblast proliferation (sensu Nematoda and Protostomia) ; GO:0043349 neuroblast proliferation (sensu Vertebrata) ; GO:0043350 neuroblast activation (sensu Nematoda and Protostomia) ; GO:0043351 neuroblast activation (sensu Vertebrata) ; GO:0043352

erythrocyte differentiation (sensu Mammalia) ; GO:0043353 erythrocyte maturation (sensu Mammalia) ; GO:0043354

epidermal cell differentiation (sensu Insecta) ; GO:0043355 epidermal cell fate specification (sensu Insecta) ; GO:0043356

Original comment by: jl242

gocentral commented 19 years ago

Logged In: YES user_id=451873

Rather than this:

**GO; add erythrocyte_(sensuMammalia), erythrocyte(sensu_non-Mammalia) as childs of of erythrocyte

we'll make the terms 'nucleate erythrocyte' and 'enucleate erythrocyte' in both GO and CL.

Original comment by: jl242

gocentral commented 19 years ago

Logged In: YES user_id=451873

Changed adipocyte -> fat cell with adipocyte as synonym.

Made 'iridophore differentiation ; GO:0050935' and 'xanthophore differentiation ; GO:0050936' children rather than siblings of 'melanocyte differentiation ; GO:0030318'.

Added new terms:

pigment cell differentiation (sensu Nematoda and Protostomia) ; GO:0043357 pigment cell differentiation (sensu Vertebrata) ; GO:0043358

glial cell migration (sensu Nematoda and Protostomia) ; GO:0043359 glial cell differentiation (sensu Nematoda and Protostomia) ; GO:0043360 glial cell fate determination (sensu Nematoda and Protostomia) ; GO:0043361

Original comment by: jl242

gocentral commented 19 years ago

Logged In: YES user_id=451873

Added new terms:

nucleate erythrocyte maturation ; GO:0043362 nucleate erythrocyte differentiation ; GO:0043363

for GO:cell ontology alignment.

GO changes now finished.

Original comment by: jl242

gocentral commented 19 years ago

Original comment by: jl242