gocentral commented 16 years ago

I'm redundantly pasting into the body AND attaching the file. Take your pick.

If manually adding these is tedious we can try a walkthrough of doing it in OE, though this will be painful for the first few iterations.

I have vetted these and am reasonably confident that they are if not correct at least consistent with what CL and GO itself says. I have commented on the dodgier ones.

"oenocyte differentiation" [GO:0001742] is_a "columnar/cuboidal epithelial cell differentiation" [GO:0002065] "T-helper cell lineage commitment" [GO:0002295] is_a "CD4-positive, alpha-beta T cell lineage commitment" [GO:0043373] "T-helper 1 cell lineage commitment" [GO:0002296] is_a "T-helper cell lineage commitment" [GO:0002295] "T-helper 2 cell lineage commitment" [GO:0002297] is_a "T-helper cell lineage commitment" [GO:0002295] "CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment" [GO:0002362] is_a "CD4-positive, alpha-beta T cell lineage commitment" [GO:0043373] "NK T cell lineage commitment" [GO:0002364] is_a "alpha-beta T cell lineage commitment" [GO:0002363] "dendritic cell cytokine production" [GO:0002371] is_a "leukocyte mediated immunity" [GO:0002443] "dendritic cell antigen processing and presentation" [GO:0002468] is_a "leukocyte mediated immunity" [GO:0002443] "myeloid dendritic cell antigen processing and presentation" [GO:0002469] is_a "myeloid leukocyte mediated immunity" [GO:0002444] "monocyte antigen processing and presentation" [GO:0002471] is_a "myeloid leukocyte mediated immunity" [GO:0002444] "macrophage antigen processing and presentation" [GO:0002472] is_a "myeloid leukocyte mediated immunity" [GO:0002444] "spermatid development" [GO:0007286] is_a "germ cell development" [GO:0007281] "neuroblast fate determination" [GO:0007400] is_a "stem cell fate determination" [GO:0048867] "oenocyte development" [GO:0007438] is_a "columnar/cuboidal epithelial cell development" [GO:0002066] "megasporogenesis" [GO:0009554] is_a "germ cell development" [GO:0007281] "auditory receptor cell fate commitment" [GO:0009912] is_a "neuron fate commitment" [GO:0048663] "epidermal cell differentiation" [GO:0009913] is_a "epithelial cell differentiation" [GO:0030855] "trichoblast differentiation" [GO:0010054] is_a "stem cell differentiation" [GO:0048863] "atrichoblast differentiation" [GO:0010055] is_a "stem cell differentiation" [GO:0048863] "atrichoblast fate specification" [GO:0010056] is_a "stem cell fate specification" [GO:0048866] "trichoblast fate specification" [GO:0010057] is_a "stem cell fate specification" [GO:0048866] "microglia differentiation" [GO:0014004] is_a "macrophage differentiation" [GO:0030225] "neuroblast differentiation" [GO:0014016] is_a "stem cell differentiation" [GO:0048863] "neuroblast fate commitment" [GO:0014017] is_a "stem cell fate commitment" [GO:0048865] "neuroblast fate specification" [GO:0014018] is_a "stem cell fate specification" [GO:0048866] "neuroblast development" [GO:0014019] is_a "stem cell development" [GO:0048864] "eurydendroid cell differentiation" [GO:0021755] is_a "neuron differentiation" [GO:0030182] "pyramidal neuron migration" [GO:0021852] is_a "neuron migration" [GO:0001764] "pyramidal neuron differentiation" [GO:0021859] is_a "neuron differentiation" [GO:0030182] "Cajal-Retzius cell differentiation" [GO:0021870] is_a "neuron differentiation" [GO:0030182] "sorocarp stalk cell differentiation" [GO:0031149] is_a "columnar/cuboidal epithelial cell differentiation" [GO:0002065] "lamellocyte differentiation" [GO:0035171] is_a "plasmatocyte differentiation" [GO:0042387] "hair cell differentiation" [GO:0035315] is_a "neuron differentiation" [GO:0030182] "photoreceptor cell development" [GO:0042461] is_a "neuron development" [GO:0048666] "auditory receptor cell differentiation" [GO:0042491] is_a "hair cell differentiation" [GO:0035315] "auditory receptor cell fate specification" [GO:0042667] is_a "neuron fate specification" [GO:0048665] "auditory receptor cell fate determination" [GO:0042668] is_a "neuron fate determination" [GO:0048664] "CD4-positive, alpha-beta T cell lineage commitment" [GO:0043373] is_a "alpha-beta T cell lineage commitment" [GO:0002363] "CD8-positive, alpha-beta T cell lineage commitment" [GO:0043375] is_a "alpha-beta T cell lineage commitment" [GO:0002363] "photoreceptor cell fate determination" [GO:0043703] is_a "neuron fate determination" [GO:0048664] "photoreceptor cell fate specification" [GO:0043704] is_a "neuron fate specification" [GO:0048665] "photoreceptor cell differentiation" [GO:0046530] is_a "neuron differentiation" [GO:0030182] "photoreceptor cell fate commitment" [GO:0046552] is_a "neuron fate commitment" [GO:0048663] "companion cell differentiation" [GO:0048758] is_a "parenchymal cell differentiation" [GO:0048760] "neuromast hair cell differentiation" [GO:0048886] is_a "hair cell differentiation" [GO:0035315] "cardiac muscle cell development" [GO:0055013] is_a "muscle cell development" [GO:0055001] "neuroblast division" [GO:0055057] is_a "somatic stem cell division" [GO:0048103] "astrocyte fate commitment" [GO:0060018] is_a "glial cell fate commitment" [GO:0021781] "radial glial cell differentiation" [GO:0060019] is_a "neuroblast differentiation" [GO:0014016] "Bergmann glial cell differentiation" [GO:0060020] is_a "astrocyte differentiation" [GO:0048708] "auditory receptor cell development" [GO:0060117] is_a "neuron development" [GO:0048666] "myeloid dendritic cell cytokine production" [GO:0002372] is_a "myeloid leukocyte mediated immunity" [GO:0002444] "ganglion mother cell fate determination" [GO:0007402] is_a "stem cell fate determination" [GO:0048867] "follicular dendritic cell differentiation" [GO:0002268] is_a "cell differentiation" [GO:0030154] "lymphocyte costimulation" [GO:0031294] is_a "immune system process" [GO:0002376]

"chlamydospore formation" [GO:0001410] is_a "anatomical structure formation" [GO:0048646] "syncytium formation" [GO:0006949] is_a "anatomical structure formation" [GO:0048646] "pole cell formation" [GO:0007279] is_a "anatomical structure formation" [GO:0048646] "oocyte construction" [GO:0007308] is_a "anatomical structure formation" [GO:0048646] "pollen wall formation" [GO:0010208] is_a "anatomical structure formation" [GO:0048646] "platelet formation" [GO:0030220] is_a "anatomical structure formation" [GO:0048646]

I don't see why not...

"oocyte dorsal/ventral axis determination" [GO:0007310] is_a "oocyte axis determination" [GO:0007309]

currently part_of. I think the xps are correct here - a DV axis is_a axis

"retinal ganglion cell axon guidance" [GO:0031290] is_a "neuron migration" [GO:0001764]

I thought this was wrong at first: movement of cell parts does not imply movement of cells;

but axon guidance is_a cell migration in GO, so perhaps this link is wrong?

* "germ cell attraction" [GO:0035232] is_a "positive chemotaxis" [GO:0050918]

"germ cell repulsion" [GO:0035233] is_a "negative chemotaxis" [GO:0050919]
I'm pretty sure these two are wrong. It's not totally clear from the chemotaxi defs

If it's wrong I'll remove the offending lines below from bp_xp_cl:

[Term] id: GO:0035232 ! germ cell attraction intersection_of: GO:0050918 ! positive chemotaxis intersection_of: OBO_REL:results_in_movement_of CL:0000586 ! germ cell

[Term] id: GO:0035233 ! germ cell repulsion intersection_of: GO:0050919 ! negative chemotaxis intersection_of: OBO_REL:results_in_movement_of CL:0000586 ! germ cell

Reported by: cmungall

Original Ticket: "geneontology/ontology-requests/4943":https://sourceforge.net/p/geneontology/ontology-requests/4943

gocentral commented 16 years ago

Original comment by: cmungall

gocentral commented 16 years ago

assigned_to: nobody --> ukemi

Original comment by: ukemi

gocentral commented 16 years ago

Logged In: YES user_id=436423 Originator: NO

> "retinal ganglion cell axon guidance" [GO:0031290] is_a "neuron > migration" [GO:0001764] > # I thought this was wrong at first: movement of cell parts does not imply > movement of cells; > # but axon guidance is_a cell migration in GO, so perhaps this link is > wrong?

It's wrong, but slated to be fixed. Doug and Michelle have worked out a new structure around cell movement/motility/etc., and we'll implement it once they've come up with some new definitions. (David knows all about this.)

m

Original comment by: mah11

gocentral commented 16 years ago

assigned_to: ukemi --> nobody

Original comment by: ukemi

gocentral commented 16 years ago

assigned_to: nobody --> ukemi

Original comment by: ukemi

gocentral commented 16 years ago

I think the axon guidance issue was supposed to be addressed recently by David's implementation of [ 1766338 ] RefGen: cilium/flagellum movement , l/r asymmetry. 'axon guidance' was to become an is_a child of 'cell motion' I believe. That change doesn't seem to have happened yet. David??

Original comment by: doughowe

gocentral commented 16 years ago

Hi Doug,

I didn't make that change. I claimed this SF as a reminder.

David

Original comment by: ukemi

gocentral commented 16 years ago

The section of GO dealing with hair cells requires reorganization. Hair cells in the CL are mechanoreceptors, the changes caused by this are as follows:

Move terms from under hair cell to GO:0009913 epidermal cell differentiation is_a GO:0035316 non-sensory hair organization and biogenesis is_a GO:0010026 trichome differentiation

Make new relations GO:0030182 neuron differentiation is_a GO:0042490 mechanoreceptor differentiation

GO:0042490 mechanoreceptor differentiation is_a GO:0035315 hair cell differentiation

GO:0035315 hair cell differentiation is_a neuromast hair cell differentiation (new term)

Auditory receptor cell should be merged into auditory hair cell in CL see tracker item 2164496 This change may mean that GO:0060113 inner ear receptor cell differentiation and GO:0042491 auditory receptor cell differentiation should be merged, their children renamed and GO:0060113 inner ear receptor cell differentiation gets 4 children inner hair cell differentiation CL:0000589 outer hair cell differentiation CL:0000601 vestibular hair cell differentiation CL:0000609 macular hair cell differentiation (new term tracker request CL 2164574)

Also in the inferred relations the following changes should be made:

auditory hair cell fate specification (renamed)[GO:0042667] is_a neuromast hair cell differentiation (new term)

auditory hair cell fate determination (renamed) [GO:0042668] is_a hair cell fate determination (new term)

auditory hair cell development (renamed) [GO:0060117] is_a hair cell development (new term)

The radial glial cell needs some reworking. Radial glial cells develop from the neuroepithelium,then provide a scaffold for migrating neurons, later give rise to both radial glial cells and neuroblasts. So radial glial cells legitimately have 2 is_a parents in the CL. Giving rise to the GO
GO:0010001 glial cell differentiation is_a GO:0060019 radial glial cell differentiation and GO:0014016 neuroblast differentiation is_a GO:0060019 radial glial cell differentiation

Also Bergmann glial cell differentiation should not be a child of radial glial cell differentiation based on CL It should be GO:0048708 astrocyte differentiation is_a GO:0060020 Bergmann glial cell differentiation

Original comment by: cerivs

gocentral commented 16 years ago

We've begun working through these. Most of them are ok and we have added the links but a few point out errors or omissions in the Cell Ontology that need to be fixed.

Original comment by: tberardini

gocentral commented 16 years ago

More work done today:

added many of the suggested relationships renamed all of the terms with 'axis determination' in the primary term to be 'axis specification' in the primary term name with 'axis determination' as exact synonyms

Note to Doug: "axon guidance" changes were made by David previously

Note to Ceri: some of your suggestions were incorporated and comments were helpful, thanks. However, wrt hair cells, in GO, hair cells encompass plant and animal cells so the relationships suggested in your comment were not made. The Cell Ontology needs to be fixed to cover plant and animal cases.

Didn't make:

"chlamydospore formation" [GO:0001410] is_a "anatomical structure formation" [GO:0048646]

because the definition and exact synonym of 1410 say that this term is chlamydospore development. Does the community say 'formation' when it really means 'development'?

Still pending:

several terms to check with Alex wrt Cell Ontology parentage

Original comment by: tberardini

gocentral commented 14 years ago

status: open --> closed

Original comment by: ukemi

gocentral commented 14 years ago

status: closed --> closed-out-of-date

Original comment by: ukemi

gocentral commented 14 years ago

Marking this as fixed, in all cases changes were made to CL or links added to GO.

Original comment by: cmungall

gocentral commented 14 years ago

status: closed-out-of-date --> closed-fixed

Original comment by: cmungall

geneontology / go-ontology

65 potential missing links in BP (from CL xps) #4928

I don't see why not...

currently part_of. I think the xps are correct here - a DV axis is_a axis

I thought this was wrong at first: movement of cell parts does not imply movement of cells;

but axon guidance is_a cell migration in GO, so perhaps this link is wrong?

I'm pretty sure these two are wrong. It's not totally clear from the chemotaxi defs

If it's wrong I'll remove the offending lines below from bp_xp_cl: