From fdelcoux at ulb.ac.be Wed Dec 7 12:25:34 2005 From: fdelcoux at ulb.ac.be (=?ISO-8859-1?Q?Fran=E7ois_Delcoux?=) Date: Wed, 7 Dec 2005 18:25:34 +0100 Subject: Feedback on POC (fwd) (PR#89) In-Reply-To: <200511170039.jAH0dtxr019582@brie4.cshl.org> References: <200511170039.jAH0dtxr019582@brie4.cshl.org> Message-ID: <205E0A13-2EAC-4D46-9764-F789BE73272A@ulb.ac.be> Hello! Sorry for anwsering you so late, but I have been very busy those last weeks. I had a talk with my boss about your demand. Since you are to make a non-profit use of my softs, you can, of course, get it for free. But, my lab wants to make a publication about it first. So you will have to wait about 6 months before being allowed to use it. Of course, you will have to cite the paper related to my tools each time you use them. In the meantime, I would gladly do your monthly merge and bug- reporting on my own, if you want me to. Yours sincerely, Fran?ois DELCOUX (ULB, Belgium) Le 17 nov. 2005 ? 01:39, Katica Ilic a ?crit : > I would like to ask if you would be willing to share this tool with > us, our > software developer would like to take a look and see if we can use > it regularly. > For us, this would be a better option than once-a-week email > notification. > Please let me know if there is proprietary or other issues related > to this. > > Regarding OWL files, I must admit, I don?t know much about it > myself, and will > leave it to our Bioinformatics group to decide whether it would be > useful to > provide to our users the OWL file of the Plant Ontology, in > addition to the > existing OBO file format. From katica at acoma.Stanford.EDU Thu Dec 8 15:54:50 2005 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Thu, 8 Dec 2005 12:54:50 -0800 (PST) Subject: Feedback on POC (fwd) (PR#89) In-Reply-To: <205E0A13-2EAC-4D46-9764-F789BE73272A@ulb.ac.be> References: <200511170039.jAH0dtxr019582@brie4.cshl.org> <205E0A13-2EAC-4D46-9764-F789BE73272A@ulb.ac.be> Message-ID: Hi Fran???ois, No problem, let us know when we can have it, our programer would like to take a look, although six month from now we are hoping to merge our two OBO files into one (like GO OBO file). Best of luck in you studies and research, Katica On Wed, 7 Dec 2005, Fran?ois Delcoux wrote: > Hello! > > Sorry for anwsering you so late, but I have been very busy those last weeks. > > I had a talk with my boss about your demand. Since you are to make a > non-profit use of my softs, you can, of course, get it for free. But, my lab > wants to make a publication about it first. So you will have to wait about 6 > months before being allowed to use it. Of course, you will have to cite the > paper related to my tools each time you use them. > > In the meantime, I would gladly do your monthly merge and bug-reporting on my > own, if you want me to. > > Yours sincerely, > Fran?ois DELCOUX (ULB, Belgium) > > > Le 17 nov. 2005 ? 01:39, Katica Ilic a ?crit : > >> I would like to ask if you would be willing to share this tool with us, our >> software developer would like to take a look and see if we can use it >> regularly. >> For us, this would be a better option than once-a-week email notification. >> Please let me know if there is proprietary or other issues related to this. >> >> Regarding OWL files, I must admit, I don?t know much about it myself, and >> will >> leave it to our Bioinformatics group to decide whether it would be useful >> to >> provide to our users the OWL file of the Plant Ontology, in addition to the >> existing OBO file format. > -- -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From SchaefferM at missouri.edu Thu Dec 15 11:16:33 2005 From: SchaefferM at missouri.edu (Mary (MaizeGDB)) Date: Thu, 15 Dec 2005 10:16:33 -0600 Subject: FYI from GO FW: A _draft_ proposal re unknown terms In-Reply-To: Message-ID: I believe we have discussed this in the PO, and the use by GO was one reason to allow in PO. However, this seems to be changing a bit. mary ------ Forwarded Message From: "Michael Ashburner (Genetics)" Reply-To: "Michael Ashburner (Genetics)" Date: Thu, 15 Dec 2005 08:52:05 +0000 (GMT) To: go at genome.stanford.edu Cc: phismith at buffalo.edu Subject: A _draft_ proposal re unknown terms GO folk and Barry. I attach a draft proposal and justification re eliminating the pesky *_unknown terms in the GO. I welcome feedback. Michael A proposal to eliminate *_unknown functions from the Gene Ontology. MA. Draft 1. December 15 2005. Each of the three axes of the Gene Ontology, molecular function, biological process and cellular component, includes an 'unknown' term, i.e., molecular function unknown ; GO:0005554 biological process unknown ; GO:0000004 cellular component unknown ; GO:0008372 The GO documentation clearly states that these nodes are to be used only when a curator has searched for information concerning a particular gene product, either computationally or in the literature, and has failed to find any evidence for a _particular_ molecular function (or biological process or cellular component). The evidence code to be used is ND (no data), unless (a) there is a literature reference which explicitely states that (e.g.) the function of the gene product is unknown (in which case use the evidence code NAS or TAS and cite the reference), or (b) when the 'unknown' property is inferred by ISS with, e.g. an InterPro domain which is itself stated to have unknown function. There has been concern about these three nodes for some time and I am now suggesting that we change both the GO and documentation to eliminate them. Instead, gene products that would (on the criteria set out above) have been annotated to these terms will now be annotated to the relevant root term, i.e., molecular function ; GO:0003674 biological process ; GO:0008150 cellular component ; GO:0005575 There is an assumption behind this proposal: it is that no gene product is wholly 'useless'. My view is that this is not an unreasonable assumption and that if there is ever rigorous evidence for a 'useless' gene product then we will cross that bridge. The reason for this change is that the three 'unknown' nodes violate a principle of ontology development. At the moment they are direct 'isa' children of their root. But this is, of course, nonsense: 'molecular function unknown' is NOT a type of 'molecular function'. This relationship is simply wrong. One of the great benefits of the subsumption hierarchy built into the GO is that objects can be annotated with a parent node, rather than a more granular leaf, so as to indicate the shallow depth of knowledge at the time of annotation. That is precisely what we are suggesting. A gene product that is now annotated with an '* unknown' term would be annotated with the root - which says 'this gene product _has_ a molecular function (etc) but we do not know anything more specific about it'. ------ End of Forwarded Message