Protein Ontology (PRO) Activity
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Activity for Protein Ontology (PRO)
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Darren Natale posted a comment on ticket #117
SN-agrin is just the canonical isoform. I added the reference and synonym. [Term] id: PR:A2ASQ1-1 name: agrin isoform m1 (mouse) def: "An agrin (mouse) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:A2ASQ1-1." [PRO:DNx, UniProtKB:A2ASQ1, PMID:11018052] comment: Category=organism-sequence. synonym: "mAGRN/iso:m1" EXACT PRO-short-label [PRO:DNx] synonym: "agrin isoform TM-agrin (mouse)" EXACT [UniProtKB:A2ASQ1] synonym: "SN-agrin...
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F8VPM9
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The first protein is identical to an existing PRO term, so I added the PMID to that term and made the TrEMBL-based accession an alt_id to the existing Swiss-Prot based PRO term. The second is an isoform of an existing PRO term, and defined accordingly. The third is a sequence variant of an existing isoform, and again defined accordingly. [Term] id: PR:Q03172 alt_id: PR:F8VPM9 name: zinc finger protein 40 (mouse) def: "A zinc finger protein 40 that is encoded in the genome of mouse." [PRO:DNx, OMA:Q03172,...
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E9PYB0
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J3QQ16
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I have created the following two terms. The first one is considered organism-sequence because it is one of many isoforms (according to MGI), and not even the longest one, and it is quite unlikely that this entry will become the canonical. The second term is also one of many isoforms, but this one is the most likely to be the canonical for mouse based on alignment with the human orthology. I have therefore defined it as an organism-gene term. [Term] id: PR:J3QQ16 name: collagen, type VI, alpha 3 isoform...
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Harold J. Drabkin posted a comment on ticket #117
I still need an id for the SN form for PMID:11018052 of Agrn (SN form)
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Also used A2AHT3 using PMID:11792319 and A2AEW1 using PMID:16936731
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Also used A2AHT3 using PMID:11792319
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Same group annotated to D3YWT3; need to move into PRO; using PMID:20044351
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The same group has used D3YX90 for annotation using PMID:22159717. Needs to be moved into PRO
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E9PYB0
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F8VPM9
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J3QQ16
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two entries in pro/id
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Closing old tickets already addressed. The issue you raised happened because the dynamic generator only looked for whatever comes before the first space, so found a valid accession when the space was present. It also 'split' the accession into two parts--one for the main accession and one for the isoform--based on a dash being present. So when the dash was there (with no space before it and no numbers after it) it again found a valid accession and ignored the lack of isoform number.
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New term request: amylase
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G protein-coupled receptor logical definition broken
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Good to know. I couldn't find it indicated in Ontobee.
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David Osumi-Sutherland posted a comment on ticket #132
Oops, didn't see David's response. I think capable_of will do. We'll make the switch for this and others. Excellent. BTW - the classification of GO MF under BFO:occurrent + many uses of capable_of should be visisble in go-plus.owl
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Oops, didn't see David's response. I think capable_of will do. We'll make the switch for this and others.
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I find the classification of functions as realizable entities and continuants perfectly reasonable. The problem you see actually is an effect of someone's unfortunate decision to class GO MFs as processes. I know there was some talk of this but didn't know it went into effect. Then again, did it? That relation is not asserted at all within the GO hierarchy, so it must be asserted outside of GO itself. Interestingly, it means that there are no targets for has_function in GO. Unintuitive indeed. Will...
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PR should use capable_of (RO_0002215) instead of has_function here. This will align with GO.
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Nicolas Matentzoglu created ticket #132
G protein-coupled receptor logical definition broken
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Hi Nicole, I have made two classes based on this request. The one you want is PR:000049996. Note that these were defined using activity as the basis rather than evolution (which is how we usually define PRO terms of this type). I did it this way because I presume you are interested in measureable amylase, and so far as I can tell, the measurement is one of activity rather than something like proteomics. Please let me know if I'm mistaken! Note also that these terms won't appear in the downloadable...
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Nicole Vasilevsky posted a comment on ticket #131
Hi Darren, I meant generic-to-humans form, thank you! Best, Nicole -- Nicole Vasilevsky, PhD Research Assistant Professor Translational and Integrative Sciences Labhttps://tislab.org/ Oregon Clinical & Translational Research Institute Department of Medical Informatics & Clinical Epidemiology Oregon Health & Science University Email: vasilevs@ohsu.edu Skype: nicolevasilevsky From: Darren Natale darren_natale@users.sourceforge.net Reply-To: "[pro-obo:term-requests]" 131@term-requests.pro-obo.p.re.sourceforge.net...
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Hi Nicole, Before we create the term you need, I'll need to have a clarification. When you say " a generic form" do you mean a generic-to-humans versions (that combines, say, human alpha amylase and human beta amylase), or do you mean fully generic, as in "any protein from any organism with amylase activity" (which would include from yeasts, bacteria, etc)?
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New term request: amylase
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H3 K9me3
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Okay, in that case, for K9 trimethylation, you want the following: hht1 PR:000044699 hht2 PR:000044702 hht3 PR:000044705 To search, you can go to the PRO main page https://proconsortium.org/pro/pro.shtml and use either the search or the SPARQL (with examples that cover the request you(?) made once upon a time on how to find all PRO entries for a specific gene). The SF tracker won't always have everything because sometimes I anticipate future needs ;)
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Valerie Wood posted a comment on ticket #130
All three is fine. We can't distinguish as they are identical, and I wnat the annotation to appear as modification on all 3 objects. v
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H3 K9me3
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It just occurred to me that I might have mis-interpreted your request. Did you want a term that covers K9-trimethylation for any of the H3 types? We have terms that cover each of the specific types (H3.1, H3.2, H3.3) but not one that covers (H3.1 or H3.2 or H3.3).
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my fault, I always forget where I can search, so I just searched in teh SF tracker. Can you remind me where I should search ? v
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H3 K9me3
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It turns out we already have the requested term! It is PR:000044705 (reproduced below). I added your additional evidence. In fact, we have K9 methylation terms for pombe H3.1, H3.2, and H3.3, and for each methylation type: non-specific, mono-, di-, and trimethylated. Sorry I didn't catch it earlier. [Term] id: PR:000044705 name: histone H3.3, initiator methionine removed K9-trimethylated form (Schizosaccharomyces pombe) def: "A histone H3.3, initiator methionine removed K9-methylated form (Schizosaccharomyces...
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Hi Darren, yes please methionine removal is fine. I think this should be the defult on all of our moified histnes since the 'active' form is demethylated? Val
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H3 K9me3
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Currently in PRO we have the following term (at bottom), which appears to be identical to what you are requesting except for two things: 1) The methylation type (mono-, di-, or tri-) is not indicated; 2) Removal of an initiator methionine is indicated. I can very quickly create a new term based on that old one (with the specific methylation type indicated), but I just need to know about the initiator methionine removal. Do you wish to have the new term have that removed, or not? Considering the definition,...
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H3 K9me3
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I cannot access the request. I think I need the name you used to put it in (or have the information in the request reproduced by email). On 8/23/2018 10:40 AM, Harold J. Drabkin wrote: [term-requests:#129] discs large homolog 2 isoform 9 (aka isoform eta) Status: open Group: Created: Thu Aug 23, 2018 02:40 PM UTC by Harold J. Drabkin Last Updated: Thu Aug 23, 2018 02:40 PM UTC Owner: Darren Natale Ceci asked me to put this RACE-PRO request here while she is away so I can get the term Reference: REF14972_A0A2L2P595,...
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discs large homolog 2 isoform 9 (aka isoform eta)
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sid4, dma1
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Thanks, you are never slow, believe me. I only created the ticket 2 days ago! This is the fastest tracker! I wanted to capture that dma1 (unubiquitinated) only binds to phosphorylated sid4 to negatively regulated SIN signalling. So the other ref was the correct one for phosphorylated sid4. Thanks for figuring that out. Val
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Hi Val, Sorry for the delay, I was away. I created a number of terms based on your request. The specific terms you requested are PR:000044611 for the phosphorylated sid4, and PR:000044743 for the unmodified dma1. A few notes on the above: 1) The paper you cite doesn't describe the phosphorylated sid4, only mentions it. I found the description in another paper. 2) Because of the above, I wondered if you actually wanted the ubiquitinated sid4. So I made it just in case. A full accounting of the entire...
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sid4, dma1
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which term for proline isomerization
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possible malformed term?
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thanks!
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Nope, just import the ones we need. The OBO Foundry website lists Henning Hermjakob (mailto:hhe@ebi.ac.uk) as the contact, but I'm pretty sure that's very old information and that it is John Garavelli (jsgarave@udel.edu) that maintains it. I followed a few links and found this tracker: https://sourceforge.net/p/psidev/mod-controlled-vocab-changes/new/
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oh gosh. Do you know who maintins PSI-MOD? I don't think I actually requested a PSI-MOD term before. I thought you did both!
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It is indeed the wrong tracker. This is the tracker for PRO. I tried anyway. ;)
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Is this the wrong tracker for PSI-MOD issues?
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It is in our Canto tool. I'll ask Kim to take a look, maybe it is truncated for some reason.
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possible malformed term?
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Can you tell me where you searched to find this? We don't use this term in PRO, and it looks fine in my copy of PSI-MOD.
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possible malformed term?
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which term for proline isomerization
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Promote trembls to full PR ids
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Hi Harold, The terms have been created. All terms were added as isoforms except where indicated. Terms with specific notes are in bold below. Let me know if you want the stanzas pasted here. A0A0R4J0I9 Lrp1 PMID:24305823 PR:A0A0R4J0I9 E9PYV8 Adamts9 PMID:20093484 PR:E9PYV8 F7AAP4 Atp2b4 PMID:18591664 PR:F7AAP4 G5E8P4 Cobl PMID:22114352 PR:G5E8P4 Q1A6U9 Inpp4b PMID:16631325 PR:Q1A6U9 Q1A6V0 Inpp4b PMID:16631325 PR:Q1A6V0 Q1A6V1 Inpp4b PMID:16631325 PR:Q1A6V1 Q3V4A2 Mospd3 PMID:11591653 PR:Q3V4A2 Q3V4B7...
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Midori Harris posted a comment on ticket #125
I know the feeling. Thanks again for another amazingly fast turnaround!
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S. pombe ras1, GTP-bound form
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Ohhh I like the easy ones :) Here are your terms, which will appear on the web immediately, and in the download with the next release (within about a month). [Term] id: PR:000036978 name: ras-like protein 1 (Schizosaccharomyces pombe) def: "A protein that is a translation product of the ras1 gene in Schizosaccharomyces pombe." [PRO:DAN] comment: Category=organism-gene. Requested by=PomBase. synonym: "Spom-ras1" EXACT PRO-short-label [PRO:DNx] synonym: "SPAC17H9.09c" RELATED [] intersection_of: PR:000000001...
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S. pombe ras1, GTP-bound form
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Answer to 1: yes; I can furnish the gene it's suppose to belong to if need. 2. The entries chosen for the GOA mouse ones are their curator decisions. We assume they know what they are doing. Even single amino acid differences may be important. I have actually put in varients into RACEPRO at times . The key here is that the ids get associated with the correct gene in MGI so that they can be used.
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I think we would still like to have the requested terms eventually, but it isn't urgent for us. "Pending" status fits our situation just fine.
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Influenza hemagglutinin
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Going through old requests and closing those that were finished long ago or marking as "pending" those that await input from the requester. If your request is marked Pending, please advise as to whether the request has been satisfactorily addressed or is no longer needed.
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NTR: vomeronasal receptor
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Going through old requests and closing those that were finished long ago or marking as "pending" those that await input from the requester. If your request is marked Pending, please advise as to whether the request has been satisfactorily addressed or is no longer needed.
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NTR: immunoglobulin superfamily
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Going through old requests and closing those that were finished long ago or marking as "pending" those that await input from the requester. If your request is marked Pending, please advise as to whether the request has been satisfactorily addressed or is no longer needed.
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ntr: GDP-bound form of pombe Spi1
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Going through old requests and closing those that were finished long ago or marking as "pending" those that await input from the requester. If your request is marked Pending, please advise as to whether the request has been satisfactorily addressed or is no longer needed.
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S. pombe protein complex terms (many)
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Going through old requests and closing those that were finished long ago or marking as "pending" those that await input from the requester. If your request is marked Pending, please advise as to whether the request has been satisfactorily addressed or is no longer needed.
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alkaline phosphatases
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Going through old requests and closing those that were finished long ago or marking as "pending" those that await input from the requester. If your request is marked Pending, please advise as to whether the request has been satifactorily addressed or is no longer needed.
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rpb1 P36594 CTD S2 phosphorylated
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Going through old requests and closing those that were finished long ago or marking as "pending" those that await input from the requester. If your request is marked Pending, please advise as to whether the request has been satifactorily addressed or is no longer needed.
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Term requests: hepatic transaminases
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Going through old requests and closing those that were finished long ago or marking as "pending" those that await input from the requester. If your request is marked Pending, please advise as to whether the request has been satifactorily addressed or is no longer needed.
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premature obsoletion of PR:000002981 ! lymphocyte antigen 76
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Sorry about the late notification. Going through and closing tickets that were resolved long ago. This term was re-activated.
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definition of amino acid chain
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Sorry for this late notification; I'm going through tickets marked open that should actually have been closed long ago. To summarize the action taken: I had very lengthy discussion with John Garavelli (of RESID fame) regarding the nature of amino acid residues, modifications thereof, and how to define amino acid chain so that it fits under the appropriate ChEBI term. The final version of amino acid chain is this: "An organic amino compound that is a polymer of amino acid chain components (unmodified...
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Dewan Mahabub Sarwar posted a comment on ticket #118
Thank you. On 22 March 2018 at 11:59, Darren Natale darren_natale@users.sourceforge.net wrote: status: open --> closed assigned_to: Darren Natale Group: --> [term-requests:#118] https://sourceforge.net/p/pro-obo/term-requests/118/ request to add proteins in the protein ontology* Status: closed Group: Created: Mon Sep 18, 2017 10:00 PM UTC by Dewan Mahabub Sarwar Last Updated: Tue Sep 19, 2017 08:49 PM UTC Owner: Darren Natale Hi, I am using Protein Ontology to discover protein models in my PhD project....
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NTR: Gonadotropin
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cleavage products of pombe sre2
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cleavage products of pombe cut1 (separase) and rad21(cohesin, kleisin subunti)
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request to add proteins in the protein ontology
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