New obol missing relationships

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A new set of missing relationships from OBOL - there are quite a few so I've divided them into 5 files with 100 missing relationships in each.

Reported by: jl242

Original Ticket: "geneontology/ontology-requests/2135":https://sourceforge.net/p/geneontology/ontology-requests/2135

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Original comment by: jl242

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Original comment by: jl242

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Original comment by: jl242

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Original comment by: jl242

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Original comment by: jl242

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I'll do number 1...

Original comment by: jl242

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I've started adding in some of the missing regulation relationship; have added the following terms as part of that error:

regulation of organismal physiological process, GO:0051239 positive regulation of organismal physiological process, GO:0051240 negative regulation of organismal physiological process, GO:0051241 positive regulation of cellular physiological process, GO:0051242 negative regulation of cellular physiological process, GO:0051243 regulation of cellular physiological process, GO:0051244 negative regulation of cellular defense response, GO:0051245

Original comment by: girlwithglasses

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obol 5 with fixed development and regulation terms removed.

Original comment by: jenclark

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remains of obol 2, 3 and 4

Original comment by: girlwithglasses

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Uploading a file of the relationships from nov 2, 3 and 4 that I haven't looked at - the others are either on the way or done.

Original comment by: girlwithglasses

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solution to the development terms in vol 5

Original comment by: jenclark

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I have fixed the development-related terms in vol 5 and uploaded a file describing my changes at the bottom of this (obol_nov_5_fixed_terms). I also uploaded a file (obol_nov_5_26Nov) with all the development lines removed and all the regulation terms removed since Amelia is fixing the regulation relationships right now. This file just contains the few lines that remain to be fixed.

Jen

Original comment by: jenclark

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all the relationships from files 2, 3, 4 and 5 added or examined and rejected apart from the following:

GO:0035203 regulation of lamellocyte differentiation is_aGO: 0045613 regulation of plasmatocyte differentiation ! GO:0035204 negative regulation of lamellocyte differentiation is_aGO:0045614 negative regulation of plasmatocyte differentiation ! GO:0035205 positive regulation of lamellocyte differentiation is_aGO:0045615 positive regulation of plasmatocyte differentiation ! -->need to check if hemocyte is a type of plasmatocyte

GO:0045670 regulation of osteoclast differentiation is_aGO:0045649 regulation of macrophage differentiation ! GO:0045671 negative regulation of osteoclast differentiation is_aGO:0045650 negative regulation of macrophage differentiation ! GO:0045672 positive regulation of osteoclast differentiation is_aGO:0045651 positive regulation of macrophage differentiation ! -->is osteoclast a type of macrophage?

GO:0007564 regulation of cuticle tanning is_aGO:0009889 regulation of biosynthesis ! GO:0045800 negative regulation of cuticle tanning is_aGO:0009890 negative regulation of biosynthesis ! GO:0045801 positive regulation of cuticle tanning is_aGO:0009891 positive regulation of biosynthesis ! -->should cuticle tanning be part of biosynthesis?

and those in the file obol_nov_234. The rest of obol_nov_5_26Nov has also been done.

Original comment by: girlwithglasses

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all the relationships from files 2, 3, 4 and 5 added or examined and rejected apart from the following:

GO:0035203 regulation of lamellocyte differentiation is_aGO: 0045613 regulation of plasmatocyte differentiation ! GO:0035204 negative regulation of lamellocyte differentiation is_aGO:0045614 negative regulation of plasmatocyte differentiation ! GO:0035205 positive regulation of lamellocyte differentiation is_aGO:0045615 positive regulation of plasmatocyte differentiation ! -->need to check if hemocyte is a type of plasmatocyte

GO:0045670 regulation of osteoclast differentiation is_aGO:0045649 regulation of macrophage differentiation ! GO:0045671 negative regulation of osteoclast differentiation is_aGO:0045650 negative regulation of macrophage differentiation ! GO:0045672 positive regulation of osteoclast differentiation is_aGO:0045651 positive regulation of macrophage differentiation ! -->is osteoclast a type of macrophage?

GO:0007564 regulation of cuticle tanning is_aGO:0009889 regulation of biosynthesis ! GO:0045800 negative regulation of cuticle tanning is_aGO:0009890 negative regulation of biosynthesis ! GO:0045801 positive regulation of cuticle tanning is_aGO:0009891 positive regulation of biosynthesis ! -->should cuticle tanning be part of biosynthesis?

and those in the file obol_nov_234. The rest of obol_nov_5_26Nov has also been done.

Original comment by: girlwithglasses

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Thanks for looking at these. I'm a little confused as to how to interpret this run. I have downloaded the files below. Do these represent the relationships that were rejected? Is there a file that shows either all rejected or all accepted relationships? 5_fixed_terms seems to have comments... help, I'm confused!!

Regarding the cell stuff: see my comments on the development list re the cell ontology - I believe GO should be in sync

Original comment by: cmungall

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It looks like it's just these to be done:

GO:0035203 regulation of lamellocyte differentiation is_aGO: 0045613 regulation of plasmatocyte differentiation ! GO:0035204 negative regulation of lamellocyte differentiation is_aGO:0045614 negative regulation of plasmatocyte differentiation ! GO:0035205 positive regulation of lamellocyte differentiation is_aGO:0045615 positive regulation of plasmatocyte differentiation ! -->need to check if hemocyte is a type of plasmatocyte

GO:0045670 regulation of osteoclast differentiation is_aGO:0045649 regulation of macrophage differentiation ! GO:0045671 negative regulation of osteoclast differentiation is_aGO:0045650 negative regulation of macrophage differentiation ! GO:0045672 positive regulation of osteoclast differentiation is_aGO:0045651 positive regulation of macrophage differentiation ! -->is osteoclast a type of macrophage?

GO:0007564 regulation of cuticle tanning is_aGO:0009889 regulation of biosynthesis ! GO:0045800 negative regulation of cuticle tanning is_aGO:0009890 negative regulation of biosynthesis ! GO:0045801 positive regulation of cuticle tanning is_aGO:0009891 positive regulation of biosynthesis ! -->should cuticle tanning be part of biosynthesis?

would that be right?

Jen

Original comment by: jenclark

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The relationships in obol_nov_234 plus those that Jen quoted still need to be looked at. I'm not sure I did anything as logical as to keep a list of the rejected relationships myself - I don't know if the others did or not.

Original comment by: girlwithglasses

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I'll write to the relevant people to find out if those relationships I pasted in should be added.

Jen

Original comment by: jenclark

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I don't think I ever finished my list (1) - I'll look it out tomorrow.

Jane

Original comment by: jl242

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Does anybody have the contact details of the new FlyBase guy? He's not on the people page yet.

Thanks,

Jen

Original comment by: jenclark

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cuticle tanning is currently part of biosynthesis so I'll add those missing regulation of cuticle tanning relationships. I've written to Alex about the others.

Jen

Original comment by: jenclark

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Shall I add this new intermediate term?

[i]regulation of biosynthesis ---[i]regulation of carbohydrate biosynthesis ------[i]regulation of polysaccharide biosynthesis ; GO:new ---------[i]regulation of cuticle tanning

The online dictionaries claim that cuticle is made of chitin and that chitin is a polysaccharide.

Thanks,

Jen

Original comment by: jenclark

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I've had a look at the nov-234 file and fixed a load of relationships. The ones that are left are uploaded below. feb-234.

Chris if we reject any suggestions should we tell you why?

Jen

Original comment by: jenclark

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latest

Original comment by: jenclark

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The reason I didn't add the cuticle tanning relationships was that I wasn't sure that cuticle tanning should be part of cuticle biosynthesis.

see def: The cross-linking of chitin and other cuticle proteins, rendering them insoluble and hardening the cuticle. This process generally darkens the color of the cuticle.

It's not really forming cuticle components from simpler substances - it's more a case of modifying the existing cuticle proteins.

Original comment by: girlwithglasses

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Yes I see your point. It seems to me from the dag as if in insect biology the 'adult' cuticle is the tanned cuticle going by the parentage. So as far as they are concerned it is a biosynthesis step in the production of adult cuticle, rather than just of cuticle. It's hard to say whether this ought just to be a developmental step though. D'y want to write to the Drosophila people and ask?

Jen

Original comment by: jenclark

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I have already - the problem is the term 'cuticle biosynthesis' - a cuticle is a structure rather than a compound, so should definitely be a development rather than biosynthesis. The problem is where to put it - Becky and I worked on this for a while (problem with pre/post embryonic I think - some is pre-, some post-) but couldn't decide. I'll see if I can find old SF item...

Original comment by: jl242

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Sounds as if that one should be diverted to that other sourceforge item then, rather than trying to solve it here. That gets rid of one more from the list.

Jen

Original comment by: jenclark

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I think that the epidermal cell differentiation term cannot be a child of the epithelial cell differentiation term since this is not true for plants. Currently the epidermis term is a generic one for all species. If there was a sensu mammal (metazoa) term then that could be part of the epithelial term.

Jen

Original comment by: jenclark

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Alex just sent a reply to my question about the differentiation terms. He says we've not to add the relationships.

Jen

Hi Jen,

Lamellocyte and plasmatocyte are fly cell types that I cannot make a judgment about.

I don't understand why obol is suggesting that GO:0045670 regulation of osteoclast differentiation should be an is_a to GO:0045649 regulation of macrophage differentiation when in the current GO, GO:0030316 osteoclast differention and GO:0030225 macrophage differentiation are both is_a's to GO:0030224 monocyte differentiation.

Although osteoclasts are sometimes thought of as bone resident macrophages, the current literature suggests they are rather a cell type related to macrophages, with both cell types derived from monocytes, and thus the current relationships in the GO seem correct to me.

From Fundamental Immunology (2003), ISBN:0781735149.

We can always change the DAG in the future if the scientific consensus changes.

Of course, a more serious problem is that monocytes are a precursor population that differentiates into macrophages, osteoclasts, and some types of dendritic cells, and we are using is_a to convey a develops_from relationship, which is not quite right. I can't solve this problem at the moment.

-- Alex

Original comment by: jenclark

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Is there anything about this item that's still up to date, or shall I close it?

Original comment by: mah11

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I think you can close it.

Jen

Original comment by: jenclark

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nobody else has commented, so I will indeed close it

Original comment by: mah11

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• status: open --> closed-fixed

Original comment by: mah11