Ontology meeting 2012-02-08
BEFORE THE MEETING
"involved_in" versus "by"
- Left over from a couple of weeks ago:
Stemming from this SF request: https://sourceforge.net/tracker/?func=detail&aid=3472406&group_id=36855&atid=440764
David questions whether the term should be
"leptin-mediated signaling pathway involved in negative regulation of appetite"
"negative regulation of appetite by leptin-mediated signaling", since the def of regulation of appetite is "any process...".
This was quickly discussed in Hinxton. Was a resolution reached? If not, maybe we can discuss it by email, and then David may record the consensus on this page please, so we have it for future reference.
I don't recall the discussion but it would be good to test both models. In one we have a chain of part_of o regulates, and this doesn't infer regulates, so the link to apetite is not direct
TermGenie gatekeeper rota
- The rota has been extended. Please see http://wiki.geneontology.org/index.php/TermGenie1_Gatekeeper_Rota
TG was not working well last week, but it seems to be better now. Heiko is working on this. Please email him if you notice problems again.
30 MINUTE MEETING
Discussion notes I: REGULATION BY
- A walk-through of creating equivalent classes in Protege, and interpreting the reasoner output.
- Have set up Webex for visuals: https://geneontology.webex.com/geneontology/j.php?ED=151371542&UID=1101234192&PW=NMzIzZDNmMTFj&RT=MTgjMjE%3D
- Will allow us to come up with rules for TG1 for creating 'regulation of x by regulation of transcription' terms. (Midori submitted a bulk load last week):
- 3483867 2012-02-03 positive regulation of transcription term
- 3483892 2012-02-03 NTR: hematopoietic stem cell migration into bone marrow
- 3483894 2012-02-03 NTR: self-proteolysis
- 3483941 2012-02-03 ntr: reg iron ion transport by reg txn
- 3483943 2012-02-03 ntr: reg meiosis by reg txn
- 3483944 2012-02-03 ntr: reg carbohydrate metab by reg txn
- 3483945 2012-02-03 ntr: -reg aa biosynth by -reg txn
- 3483946 2012-02-03 ntr: +reg DNA repair by +reg txn
- 3483947 2012-02-03 ntr: reg cell separation by reg txn
- 3483948 2012-02-03 ntr: reg conjugation by reg txn
- 3483949 2012-02-03 ntr: reg cellular resp to oxid stress by reg txn
- 3483950 2012-02-03 ntr: reg histone modification by reg txn
- 3483951 2012-02-03 ntr: +reg ergosterol biosynth by +reg txn
- 3483953 2012-02-03 ntr: +reg phospholipid biosynth by +reg txn
- 3483954 2012-02-03 ntr: reg cell cycle cytokinesis by reg txn
- 3483955 2012-02-03 ntr: reg fungal cell wall biogenesis by reg txn
- 3483956 2012-02-03 ntr: reg 4,6-pyruvyl-yada biosynth by reg txn
- 3483957 2012-02-03 ntr: -reg transmembrane transport by -reg txn
- 3484044 2012-02-03 NTR attachemtn of chromatin to nuclear envelope
- I tried creating the reciprocal terms (regulation of carbohydrate metabolism by regulation of transcription/regulation of transcription by regulation of carbohydrate metabolism) but the Reasoner obviously thought they were equivalent (I tried making new equivalence statements, and copying them from existing similar terms). Can we use 'starts with: regulation of transcription. ends with: regulation of carbohydrate metabolism, as Jane previously suggested as a solution?. I couldn't get the formatting right for this to work (Becky).