And, yes, we promise to put the documentation up on the wiki.<br><br>:)<br><br>Tanya<br><br><div class="gmail_quote">On Mon, Apr 6, 2009 at 2:50 PM, David Hill <span dir="ltr"><<a href="mailto:dph@informatics.jax.org">dph@informatics.jax.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Chris,<br>
<br>
Just for clarity. Tanya and I are currently trying to change all the 'during' terms to 'involved in' terms if there really is a part_of relationship. There are some cases in the GO where 'during' really means during. In those cases, the term means that the 2 processes just occur at the same time, but otherwise are unrelated. So the 'during' rule might not be such a good one.<br>
<br>
We need to clean up these 'during' terms as well as 'by' terms and 'via' terms.<br>
<br>
David<br>
**<div><div></div><div class="h5"><br>
Chris Mungall wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
The answer is it's a mix, depending on the xp set. *Ultimately* the goal is to never have to parse a term again and to create xp defs prospectively rather than retrospectively (we can still use obol for *generation* of names, defs and synonyms, based on the newly created xp def). We're nearer this goal with some xp sets rather than others.<br>
<br>
For example, the inter-organism regulation ones are quite hard, and we probably have a few iterations to go. These iterations are quite useful besides improving the grammar, as they clarify many parts of the ontology, and also consistency of naming.<br>
<br>
The bp_xp_self which you are working on is a special case. There is a long tail of terms that can be trivially parsed; for example "X during Y" is translated to "an X that part_of Y". These have a high accuracy. But there are other terms in your set for which I liberally applied grammatical rules I knew to be less accurate. One such rule involved using a relational adjective to guess an xp def, resulting in<br>
<br>
GO:0048007 ! antigen processing and presentation, exogenous lipid antigen via MHC class Ib<br>
synonym: "exogenous lipid antigen processing and presentation via MHC class Ib" ==><br>
intersection_of: GO:0048003 ! antigen processing and presentation of lipid antigen via MHC class Ib<br>
intersection_of: part_of GO:0042638 ! exogen<br>
<br>
(currently in the vetted file)<br>
<br>
This is quite obviously wrong!! I knew there would be many incorrect ones in the bp_xp_self set from the outset, I did a first pass filter myself, but probably not a good enough job. So in some ways your set is the hardest as it has the highest ratio of nonsense. We should perhaps invert the procedure for you, such that everything starts off unvetted and must be explicitly vetted.<br>
<br>
The goal in this case is not to improve the obol rule: it's simply not possible to get a 100% accurate xp def from terms such as this. Obol is really for the low hanging fruit (LHF), the trivially composable terms.<br>
<br>
We'll probably revisit the example above when we return to do bp_xp_pro. For now, just delete erroneous xp defs such as the one above<br>
<br>
On Apr 6, 2009, at 5:27 AM, Jennifer Deegan (nee Clark) wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
David and I were editing some of my cross products together on Friday and we realised that we had different ideas of what we were meant to do. I just wanted to check that we are on the right lines now, and Chris asked me to do it on list so we are all up to date on the correct scheme.<br>
<br>
I had assumed that the intersection files that Chris generated with obol were a one-off, and that we were to hand edit the stanzas and put the resulting corrected intersection tags into the vetted file.<br>
<br>
David thought that the plan was for us to correct the live GO and feed back on obol's rules so that autogeneration would work correctly for all future runs.<br>
<br>
Which one is right?<br>
<br>
Thanks,<br>
<br>
Jen<br>
<br>
<br>
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</blockquote>
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<br></div></div><font color="#888888">
-- <br>
David P. Hill, Ph.D.<br>
Bioinformatics Scientist: Ontology Development<br>
Gene Ontology Consortium<br>
The Jackson Laboratory<br>
<a href="http://www.geneontology.org" target="_blank">www.geneontology.org</a><br>
<a href="http://www.informatics.jax.org" target="_blank">www.informatics.jax.org</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Tanya Berardini<br>TAIR Curator<br><a href="http://www.arabidopsis.org">www.arabidopsis.org</a><br>