[Obo-cell-type] GO and Cell ontologies
Pankaj Jaiswal
pj37 at cornell.edu
Wed Apr 20 10:59:53 EDT 2005
If you all agree, for plants perspective, my suggestion is that all the
plant cell instances and their nomenclature be made consistent with the
terms coming from Plant Ontology project. This will help us to create
equivalences in a automated way if not manually.
Synergid
http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0000191&show_associations=terms
Egg cell
http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0020094&show_associations=terms
Pankaj
J Clark wrote:
> Hi Michael,
>
> That all seems good to me.
>
> From the plant perspective I have checked a couple of text books and
> the 'egg cell' is always referred to fully as the 'egg cell' not just
> the 'egg'. The 'synergids' can be referred to as 'synergids' or
> 'synergid cells' so 'synergid' would be fine.
>
> Hope that helps,
>
> Jen
>
>
> Michael Ashburner (Genetics) wrote:
>
>> Both the GO and OBO CELL lists will have seen traffic recently concerning
>> the fact that GO and CL are out of synchrony with respect to the
>> semantics
>> and relationships of cell types. We must be committed to resolving
>> these problems.
>> I see this as proceeding in several steps.
>>
>> Step 1. Address the semantic differences between GO and CL with respect
>> to cell types, and differences in synonomy.
>> These are the major subjects of this email and I thank Chris & Mikel
>> Aranguren for most of the examples.
>>
>> I would like comments on these proposed changes to both CL and GO,
>> from Jonathan,
>> Sue Rhee and GO folk. Then, I and perhaps Jane will coordinate the
>> changes
>> to the two ontologies.
>>
>> The next step will be to resolve differences in
>> relationship/parenthood between
>> GO and CL and to resolve the proplems of 1 to many mappings from GO to
>> CL.
>>
>> We will then need to bring the GO and CL definitions into synchrony.
>>
>> When we think we have done all of these, I guess the next will be for
>> Chris
>> to re-run his scripts and see what we have missed.
>>
>> Then, I hope, we will be in a very good state for cross-product computes.
>>
>> Thankyou for your help - Michael
>> ======================================================================
>> Changes to CL:
>>
>> 1. REMOVE all _ and replaced by spaces.
>> 2. CORRECT spelling 'sperm cel' (synonym of CL:0000019).
>> 3. CHANGE default-namespace: to 'cell' from 'cell_ontology'.
>> 4. CHANGE all 'fat cell' to 'apidocyte' (with 'fat cell' as synonym)
>> to bring in line with GO use.
>> 5. ADD parent 'cardioblast ; CL:NEW' for 'cardioblast (sensu Arthropoda)
>> 6. ADD as isa child of 'crystal cell':
>> embryonic crystal cell
>> lymph gland crystal cell
>> 7. 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
>> 8. ADD 'female gametophyte egg cell' as isa child of 'egg cell'
>> 9. CHANGE 'epithelial cell of trachea' to 'tracheal epithelial cell'
>> 10. 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
>> This all from Gray's page 123.
>> 11. ADD 'male gametophyte sperm cell ; CL:NEW' as isa of 'sperm cell
>> (sensu Viridiplantae'
>> 12. [removed]
>> 13. CHANGE 'central cell' > 'female gametophyte central cell' (plant
>> cell)
>> 14. ADD 'NT cell' as synonym of 'natural killer cell'
>> 15. 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
>> 16. MAKE 'osteoclast' and 'macrophage' both is_a's of 'monocyte'
>> 17. ADD 'eye photoreceptor cell ; CL:NEW' as isa 'photoreceptor cell'
>> 18. ADD 'retinal cone cell ; CL:NEW' as isa 'cone cell'
>> 19. MAKE 'trichome' also an isa of 'hair cell'
>> 20. CHANGE: 'blood platelet' > 'platlet' [I presume there is no other
>> type of platlet ?]
>> 21. GO uses 'sperm', CL used 'spermatozoan'. I suggest CL changes the
>> primary term
>> to 'sperm'
>> 22. 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.
>> =========================================================================
>> Need to decide with GO:
>>
>> 0. B cell vs B-cell vs B lymphocyte
>> T cell vs T-cell vs T lymphocyte
>> T-helper vs helper T' etc
>> natural killer vs NK etc
>>
>> =========================================================================
>> Problems to be discussed with GO:
>>
>> 1. GO has the term 'thymocyte differentiation' defined as:
>> '* Processes by which a relatively unspecialized hemopoietic stem cell
>> acquires the specialized features of a thymocyte, a lymphocyte found
>> in the thymus.'
>>
>> How does this fit into CL ?
>>
>> 2. [removed]
>> 3. I suggest all GO instances of 'mesoderm cell' be changed to
>> 'mesodermal cell' [similarly ectoderm, endoderm cell, if such exist in
>> GO]
>>
>> 4. GO to change 'tracheal cell *' to 'tracheal epithelial cell *'
>> 5. GO to change 'ovarian cumulus cell differentiation' to 'cumulus
>> cell differentiation'
>> 6. GO to change 'auditory hair cell' to 'auditory receptor cell'
>> 7. GO to change 'branch cell fate determination (sensu Insecta) ->
>> branched_duct_epithelial_cell fate determination (sensu Insecta)'
>> 8. Is the GO usage of 'hemocyte' arthropod specific ? In this case
>> GO needs to change 'hemocyte differentiation (sensu Arthropoda)' by
>> removing
>> the sensu.
>> 9. GO should add neuroblast_(sensu_Nematoda_and_Protostomia),
>> neuroblast_(sensu_Vertebrata) as childs of neuroblast [cell] * terms
>> 10. GO should add erythrocyte_(sensu_Mammalia),
>> erythrocyte_(sensu_non-Mammalia) as
>> childs of of erythrocyte * terms
>> 11. Does GO need epidermal_cell_(sensu_Insecta) * as childs of
>> epidermal cell * terms ?
>> 12. ditto glial cell (sensu Nematoda and Protostomia) as childs of
>> glial cell * terms ?
>> 13. ditto pigment cell (sensu Nematoda and Protostomia), pigment cell
>> (sensu Vertebrata) as childs of pigment cell * terms ?
>> 14. The following terms in GO have 'cell' as a suffix. This suffix
>> should be removed
>> from all terms:
>> basophil cell
>> egg cell
>> hemocyte cell
>> neuroblast cell
>> neuron cell
>> oocyte cell
>> spermatid cell
>> spermatocyte cell
>> synergid cell
>> trichome cell
>> 15. 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'
>> 16. GO has 'cone cell' and 'retinal cone cell' ... are these different
>> ? i.e.
>> are their any non-retinal cone cells ? CL just has 'retinal cone cell'
>> 17. GO has both 'glia cell' and 'glial cell'. Change all former to
>> 'glial cell'
>> 18. GO has 'border cell', CL has 'border follicle cell'. I suggest GO
>> uses
>> the latter term.
>> 19. [removed]
>> 20. GO has 'cardioblast', CL 'cardioblast (sensu Arthropoda)'. Are all
>> cardioblasts Arthropod, which case CL can change and drop the sensu.
>> If not
>> then GO needs to change.
>> 21. Go has both 'leukocyte cell' and 'leukocyte'. I suggest we change all
>> former to latter.
>> 22. GO has both 'mesoderm cell' & 'mesodermal cell'. I suggest we
>> change all
>> former to latter.
>> 23. GO should change all 'neuronal cell' to 'neuron'
>> 24. GO has 'spermatogonial cell', CL has 'spermatogonium'. I suggest
>> GO changes to latter
>> ===========================================================================
>>
>> These are NOT problems [this list mainly for Chris]:
>>
>> rhabdomere development .. The reason being is that 'rhabdomere' is
>> part_of a photoreceptor cell
>> missing seed ... not a cell
>> missing sex ... not a cell
>> synonym stalk cell .. I think GO & CL are consistent
>> synonym pigment cell .. I think GO & CL are consistent
>> synonym nurse cell .. I think GO & CL are consistent
>> synonym muscle cell .. I think GO & CL are consistent
>> missing cell homeostatic ... not a cell
>> missing cell mass cell ... eh ?
>> missing positive ... eh ?
>> missing host cell ... not a cell type
>> missing epidermal cell ... GO & CL consistent
>> missing endothelial cell ... GO & CL consistent
>> missing epithelial cell ... GO & CL consistent
>> missing crest cell .. no GO has only 'neural crest cell'
>> consistent with CL
>> missing heterophilic cell ... not a cell type
>> missing homophilic cell ... not a cell type
>> missing inductive cell ... not a cell type
>> missing kinase C ... not a cell type
>> missing antipodal cell ... GO & CL consistent
>> missing central cell ... GO & CL consistent
>> missing crystal cell ... GO & CL consistent
>> missing dendritic cell ... GO & CL consistent
>> missing female gamete ... GO & CL consistent
>> missing female sex ... eh ?
>> missing female germ cell ... GO & CL consistent
>> missing follicle cell ... GO & CL consistent
>> missing garland cell ... GO & CL consistent
>> missing germ cell ... GO & CL consistent
>> missing guard cell ... GO & CL consistent
>> missing guard mother cell ... GO & CL consistent
>> missing hyphal cell ... GO & CL consistent
>> missing male gamete ... GO & CL consistent
>> missing male germ cell ... GO & CL consistent
>> missing male sex ... not a cell
>> missing mast cell... GO & CL consistent
>> missing microglial cell... GO & CL consistent
>> missing mother cell .. not in GO, though 'guard mother'
>> and 'ganglion mother' are and are consistent with CL
>> missing phospholipase C ... not a cell
>> missing ocellus ... not a cell
>> missing neural crest cell ... GO & CL consistent
>> missing pericardial cell ... GO & CL consistent
>> missing pole cell ... GO & CL consistent
>> missing protein kinase C ... not a cell
>> missing retinal cone cell ... GO & CL consistent
>> missing smooth muscle cell ... GO & CL consistent
>> missing spermatid nuclear ... eh ? .. spermatid is in CL
>> missing stem cell ... GO & CL consistent
>> missing tryptophan hydroxylase ... not a cell
>>
>>
>> ===========================================================================
>>
>> These cells are already in CL:
>>
>> natural killer cell differentiation (CL:0000623)
>> ===========================================================================
>>
>>
>> GO has these cell types not in CL - ideas on what
>> to do ?. I have grouped the immunology terms at top. There may be some
>> redundancy with what is above.
>>
>>
>> missing B-1 B-cell
>> missing NK T-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 extrathymic T-cell
>> missing helper cell
>> missing cytotoxic T-cell
>> missing gamma-delta T-cell
>> missing immune cell
>> missing killer cell
>> missing myeloid blood cell
>> missing natural killer cell
>> missing negative extrathymic T-cell
>> missing negative thymic T-cell
>> missing positive extrathymic T-cell
>> missing positive thymic T-cell
>> missing thymic T-cell
>> missing thymocyte
>> missing regulatory T-cell
>>
>> missing abaxial cell
>> missing ameboid cell
>> missing anterior cone cell
>> missing aortic cell (sensu Insecta)
>> missing autophagic cell
>> missing axial mesoderm cell
>> missing azurophil
>> missing blood cell
>> missing cardiac cell
>> missing cystoblast cell
>> missing early stripe melanocyte
>> missing edge cell
>> missing embryonic crystal cell
>> missing embryonic hemocyte
>> missing embryonic plasmatocyte
>> missing equatorial cone cell
>> missing eye photoreceptor cell
>> missing gametophyte central cell
>> missing gametophyte egg cell
>> missing gametophyte sperm cell
>> missing gland cell
>> missing gland crystal cell
>> missing gland hemocyte
>> missing gland plasmatocyte
>> missing heart proper cell
>> missing inner cell mass cell
>> missing intermediate mesoderm cell
>> missing iridophore
>> missing larval midgut cell
>> missing late stripe melanocyte
>> missing lateral mesoderm cell
>> missing leading edge cell
>> missing leukocyte
>> missing lymph gland crystal cell
>> missing lymph gland hemocyte
>> missing lymph gland plasmatocyte
>> missing male gametophyte sperm cell
>> missing mass cell
>> missing midgut cell
>> missing mystery cell fate
>> missing non-eye photoreceptor cell
>> missing organ precursor cell
>> missing paraxial mesoderm cell
>> missing polar cone cell
>> missing polarized epithelial cell
>> missing pollen
>> missing pollen germ cell
>> missing posterior cone cell
>> missing precursor cell
>> missing primary cell
>> missing primary endosperm
>> missing primary pigment cell
>> missing retinal cell
>> missing root epidermal cell
>> missing salivary gland cell
>> missing secondary cell
>> missing secondary pigment cell
>> missing sensory organ precursor cell
>> missing somatic stem cell
>> missing stripe melanocyte
>> missing tertiary pigment cell
>> missing tracheal cell
>> missing trophectoderm cell
>> missing urothelial cell
>>
>>
>>
>>
>>
>>
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>
>
--
************************
Pankaj Jaiswal, PhD
G15-Bradfield Hall
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA
Tel: +1-607-255-3103
+1-607-255-4109
Fax: +1-607-255-6683
http://www.gramene.org
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