Activity for Darren Natale
-
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...
-
F8VPM9
-
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,...
-
E9PYB0
-
J3QQ16
-
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...
-
two entries in pro/id
-
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.
-
New term request: amylase
-
G protein-coupled receptor logical definition broken
-
Good to know. I couldn't find it indicated in Ontobee.
-
Oops, didn't see David's response. I think capable_of will do. We'll make the switch for this and others.
-
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...
-
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...
-
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)?
-
H3 K9me3
-
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 ;)
-
H3 K9me3
-
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).
-
H3 K9me3
-
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...
-
H3 K9me3
-
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,...
-
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,...
-
sid4, dma1
-
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...
-
which term for proline isomerization
-
possible malformed term?
-
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/
-
It is indeed the wrong tracker. This is the tracker for PRO. I tried anyway. ;)
-
possible malformed term?
-
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.
-
Promote trembls to full PR ids
-
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...
-
S. pombe ras1, GTP-bound form
-
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...
-
Influenza hemagglutinin
-
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.
-
NTR: vomeronasal receptor
-
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.
-
NTR: immunoglobulin superfamily
-
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.
-
ntr: GDP-bound form of pombe Spi1
-
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.
-
S. pombe protein complex terms (many)
-
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.
-
alkaline phosphatases
-
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.
-
rpb1 P36594 CTD S2 phosphorylated
-
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.
-
Term requests: hepatic transaminases
-
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.
-
premature obsoletion of PR:000002981 ! lymphocyte antigen 76
-
Sorry about the late notification. Going through and closing tickets that were resolved long ago. This term was re-activated.
-
definition of amino acid chain
-
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...
-
NTR: Gonadotropin
-
cleavage products of pombe sre2
-
cleavage products of pombe cut1 (separase) and rad21(cohesin, kleisin subunti)
-
request to add proteins in the protein ontology
-
PR:Q7TSK9 is an entry you requested last week. It shows up as a regular entry because it is in the pro_wv file. I get the same result no matter which way I search, unless I add a dash at the end (with a space between as you show above, or without the space). Technically that should return an "invalid ID" error instead of a dynamically-generated page. I'll have to look into it.
-
Hi Harold Two quick questions: 1) Some of these (for example Q9D7Q2) do not have a Swiss-Prot parent term. In such cases are these to be treated as isoforms even though they can (potentially) become the "main" entry for the encoding gene in mouse? 2) How were the specific TrEMBL entries chosen? Did they map specifically to the paper? I ask because in some cases there are multiple sequence variants from the indicated gene, and only one of them would be an exact match to the reference proteome. For...
-
Promote PR:Q7TSK9
-
Here is the PRO term, now live: [Term] id: PR:Q7TSK9 name: solute carrier family 2, facilitated glucose transporter member 9 isoform Q7TSK9 (mouse) def: "A protein that is encoded by the mouse Slc2a9 gene and is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q7TSK9." [PRO:DAN, PRO:HJD, UniProtKB:Q7TSK9, PMID:14657010] comment: Category=organism-sequence. synonym: "mSlc2a9/iso:Q7TSK9" EXACT PRO-short-label [PRO:DAN] synonym: "GLUT9a(Delta209-316)"...
-
The issue is now resolved. It was due to a quirk in the timing of this release (that is, how long it's taking between the generation of the ontology files and the actual release, which is longer this time around due to some format changes we had to do). However, I have confirmed that the link you mentioned will NOT work. Again, that's due to how we have to handle those three cases I mentioned above. The PURL will work, though.
-
As for most OBO Foundry ontologies, we do not recommend using anything other than the PURL, which in the example case would be http://purl.obolibrary.org/obo/PR_000044735 We've now identified the source of the problem. Will keep you updated as to when it is resolved.
-
I don't recall if that particular link should work; I think it should. We have three cases of identifiers in PRO. First are terms already in the public release, second are terms found only in the between-releases file, and third are terms based on UniProtKB entries that are not in any file. I know for sure that the link you indicate would work if the term was of the first type. However, yours is of the second type. Our procedure handles these a bit differently, at least in the lookup stage. I know...
-
I have created the following terms. The first is the pombe pol II protein itself, and the rest are the individual modified (or not) forms. The numbering of the modified forms will be odd because there are existing terms for human orthologs, and we try to keep the numbering the same to avoid confusion. I didn't create the catch-all terms because I believe you would simply annotate to the individual ones anyway. If you do want the catch-alls, I can create them as well. PR:000044736 = gene-level term...
-
The only other question I have is whether or not you want terms for phosphorylations at other positions (like S5 or S7), and a term for the unphosphorylated form as well. If you are interested in catch-all terms, I could make a "S2P or S5P" version for the binding-competent form, and a "S7P or non-phosphorylated" version for the form that isn't bound.
-
rpb1 P36594 CTD S2 phosphorylated
-
Please take a look at http://purl.obolibrary.org/obo/PR_000048846 for how we handled it for the human ortholog. In your case it would just be position 2 that is specified. If this is suitable I'll go ahead and make the appropriate pombe version.
-
S. pombe cdc12 phosphorylated form
-
Hi Val, I've generated two terms: one is the parent cdc12 in pombe (as opposed to the strain-specific version given by PR:) and one is the requested term. Please let me know if you'd also like the strain-specific version as well. [Term] id: PR:000044734 name: cell division control protein 12 (Schizosaccharomyces pombe) def: "A protein that is a translation product of the cdc12 gene in Schizosaccharomyces pombe." [PRO:DAN] comment: Category=organism-gene. Requested by=PomBase. synonym: "Spom-cdc12"...
-
Thanks Val. Considering the name change, and based on the description in the indicated reference, I've made a few modifications. These are summarized directly below, followed by the revised stanzas. 1) Renamed the full-length protein as you indicated, and added a note mentioning that this form is an inactive precursor. 2) Renamed the N-terminal portion as ubiquitin-like protein Sde2UBL. I could not find any data showing that this part is a bona fide ubiquitin (it probably isn't), but it definitely...
-
Hi Val, We do monitor changes to UniProtKB, though there can be a lag to it. In this case, though, there would be no update because your requested term is not really from UniProt (which has the strain specific term; in PRO it is PR:O14113). So, I will make the change here and now. Just to be clear, did you include the ubiquitin fold part as name of the protein? I ask because that doesn't really impart any specificity or functional information (meaning that the first part of your proposed name is...
-
Dear Val, I've created three terms for you, representing the full-length and each requested cleavage product. Please let me know if you'd like any revision to the names for the cleavage products, for example by including the 'parent' name. [Term] id: PR:000044728 name: telomere maintenance protein SDE2 (Schizosaccharomyces pombe) def: "A protein that is a translation product of the sde2 gene in Schizosaccharomyces pombe." [PRO:DAN, UniProtKB:O14113] comment: Category=organism-gene. Requested by=PomBase....
-
N and T terminal parts of Sre2
-
Thank you for using PRO! I have added the terms you requested. The OBO format stanzas are given below (though some line wrapping will occur). Each of the terms have been curated and will appear on the PRO entry page (which will differ from the automatically-generated version). However, they will not yet be visible in the PRO download other than the limited-scope work-in-progress version, available now at http://pir.georgetown.edu/projects/pro/pro_wv.obo). Best regards, Darren Natale [Term] id: PR:P11170...
-
I should probably add my notes to this thread. I formatted an Excel spreadsheet. I find that at least one gene is likely incorrect, and there are some surprises because of a bug in the dynamic generator that fails to report when the term already exists in PRO but under a different accession. I would check all these by hand, including alignments and checks of UniParc.
-
Looking at a few of these, I note that they cannot be made automatically, and cannot be simply imported from the dynamic term maker.
-
PR:Trembl records to allow in files
-
And, just to attack on two fronts, the change-over from the current orthology-based PRO-short-labels to the organism-specific gene-based labels has been approved. These should go live in our next release (which, just so you don't get too excited, has not yet been scheduled--figure about a month).
-
Hi Val, Midori, I tought myself how to do SPARQL queries, at least enough to create the ones you need. If you go to the page http://pir.georgetown.edu/pro/pro_sparql.shtml there are a number of example queries. Each is designed to do some common database retrieval. The two at the bottom (#12 and #13) will be of most interest to you. #12 will return all PRO terms that represent proteins encoded by a particular gene of interest (which must be entered as a model organism database identifier). #13 is...
-
You're welcome! We appreciate that you use PRO!
-
S. pombe cdc42, GTP-bound form
-
I have created two new terms, one for the generic cdc42 for NCBITaxon:4896, and one for the GTP-bound form. [Term] id: PR:000044798 name: cell division control protein 42 (Schizosaccharomyces pombe) def: "A cell division control protein 42 that is encoded in the genome of Schizosaccharomyces pombe." [PRO:DAN] comment: Category=organism-gene. Requested by=PomBase. synonym: "Spom-cdc2" EXACT PRO-short-label [PRO:DNx] synonym: "SPAC110.03" RELATED [] intersection_of: PR:000005204 ! cell division control...
-
Hi Val, Midori, The PRO-short-label is designed to give some indication of orthology,...
-
My sincerest apoloties for not getting back to you sooner. I somehow had it in my...
-
Hi Val, Can you provide a few examples of PRO terms that have the gene name somewhere?...
-
Can you provide a bit more information? In particular, about the synthetic proteins,...
-
Attached. Hopefully this has no errors in it. I used Protege to convert the OBO file...
1 >