Ontology meeting 2012-05-30

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MINUTES: TANYA

30-minute call


FOLLOW-UP ON CHEBI ALIGNMENT

  • Note that the next ChEBI release is scheduled for this coming Friday, June 1st. Some of the ChEBI terms that we requested recently have been merged with other ChEBI entries, and this will be reflected in the next release, possibly rendering some xps 'silent'. Shall we look in OBOEdit again so we can make sure that no xps are left behind?
  • AI: YES! Look again in OE to make sure No Cross-product Is Left Behind.
  • AI: Standard reasoner report generated by Jenkins on June 2/3. Different results may be present.
   EXISTS, ENTAILED The link is asserted in GO but is essentially redundant, as it can be re-inferred from go_xp_chebi and chebi
   EXISTS, NOT-ENTAILED The link is asserted in GO but can NOT be re-inferred from go_xp_chebi and chebi. This might indicate a missing link in CHEBI, or the link in GO is incorrect.
   Note that these lines are also included in a separate report go-non-entailed-assertions.txt
   EXISTS, REDUNDANT May want to make link to the more specific term that it suggests.
   NEW, INFERRED A proposed new assertion for GO, inferred by the reasoner. In future, these will automatically be included in the GO build
   NEW, TRANSLATED You can ignore this; a side-effect of the oort build is to make additional assertions for all equivalence axioms
   REDUNDANT Links in GO that can be removed - these probably have nothing to do with go_xp_chebi but are reported here anyway
  • Need a smooth way, SOP, to deal with new ChEBI releases.
  • Point bio-chebi file to a specific ChEBI release. Ideally, they would provide a standard owl file for our use. Chris/Jane will follow up with Janna.
  • Use ChEBI-latest for TG. That way new ChEBI terms that are requested can be used right within a day for TG creation. Ask non-GO editors to put 'for GO terms' into their ChEBI term request to expedite addition to ChEBI.
  • T/D still need to look at non-supported links.

FOLLOW-UP ON CHEBI PAPER

punt to next week

FOLLOW-UP ON TERMGENIE PAPER

punt to next week

GETTING BP/CC TRANSPORT XPS INTO LIVE GO

  1. The existing file needs to be regenerated as several XPs are missing. E.g. 'peroxisome transport ; GO:0043574'
  2. These are the observations from a first-pass look at the existing file in: go/scratch/xps/biological_process_xp_cellular_component.obo
  3. Review relation ontology for process. http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/xps/relations_process_xp.obo


results_in_transport_of (21 occurences)

  • Should the following two GO terms changed to 'localization' term names, to match the 'organelle localization' terms?
  • Revisit. Need to make sure we don't lose specificity by changing term name.
[Term]
id: GO:0032402 ! melanosome transport
intersection_of: GO:0006810 ! transport
intersection_of: results_in_transport_of GO:0042470 ! melanosome
[Term]
id: GO:0051904 ! pigment granule transport
intersection_of: GO:0006810 ! transport
intersection_of: results_in_transport_of GO:0048770 ! pigment granule
  • GO:0006928 looks like an odd movement:
!!! TODO - use more generic relation
[Term]
id: GO:0048870 ! cell motility
intersection_of: GO:0006928 ! cellular component movement
intersection_of: results_in_transport_of GO:0005623 ! cell

results_in_transport_from (20 occurences)

  • Export is represented differently, depending on the specificity of the GO term… does this matter/is there a better way?
  • Logically the same, differences apparent when viewed in OE and integrated into main ontology.
  • Good to standardize for when we integrate other ontologies.
  • Try to fully expand to extent that is possible. Be consistent. Don't worry too much because automation could be possible.
[Term]
id: GO:0000055 ! ribosomal large subunit export from nucleus
intersection_of: GO:0051168 ! nuclear export
intersection_of: results_in_transport_of GO:0015934 ! large ribosomal subunit
[Term]
id: GO:0051168 ! nuclear export
intersection_of: GO:0006810 ! transport
intersection_of: results_in_transport_from GO:0005634 ! nucleus
[Term]
id: GO:0032974 ! amino acid export from vacuole
intersection_of: GO:0032973 ! amino acid export ***
intersection_of: results_in_transport_from GO:0005773 ! vacuole
***will expand to intersection of: results_in_transport_of: amino acid, intersection of: export

results_in_transport_to (38 occurences)

  • Different representation of import (see above for export)
[Term]
id: GO:0051170 ! nuclear import
intersection_of: GO:0006810 ! transport
intersection_of: results_in_transport_to GO:0005634 ! nucleus
[Term]
id: GO:0032975 ! amino acid import into vacuole
intersection_of: GO:0043090 ! amino acid import
intersection_of: results_in_transport_to GO:0005773 ! vacuole
[Term]
id: GO:0006608 ! snRNP protein import into nucleus
intersection_of: GO:0017038 ! protein import
intersection_of: results_in_transport_to GO:0005634 ! nucleus
intersection_of: results_in_transport_of GO:0030532 ! small nuclear ribonucleoprotein complex


results_in_transport_towards (2 occurences)

[Term]
id: GO:0006626 ! protein targeting to mitochondrion
intersection_of: GO:0006605 ! protein targeting
intersection_of: results_in_transport_towards GO:0005739 ! mitochondrion
[Term]
id: GO:0000042 ! protein targeting to Golgi
intersection_of: GO:0006605 ! protein targeting
intersection_of: results_in_transport_towards GO:0005794 ! Golgi apparatus
  • SUGGESTED TO_DO: scrap 'results_in_transport_towards', and change XPs to 'results_in_transport_to'. Can't see a difference between 'towards' and 'to'.
  • AI: Collapse for now. Run reasoner and see how many relationships can be re-inferred and how many are lost.

results_in_transport_involving (5 occurences)

[Term]
id: GO:0007041  ! lysosomal transport
intersection_of: GO:0006810 ! transport
intersection_of: results_in_transport_involving GO:0005764 ! lysosome
[Term]
id: GO:0016197  ! endosome transport
intersection_of: GO:0006810 ! transport
intersection_of: results_in_transport_involving GO:0005768 ! endosome
[Term]
id: GO:0048199 ! vesicle targeting, to, from or within Golgi
intersection_of: GO:0006903 ! vesicle targeting
intersection_of: results_in_transport_of GO:0005798 ! Golgi-associated vesicle
intersection_of: results_in_transport_involving GO:0005794 ! Golgi apparatus
[Term]
id: GO:0070296 ! sarcoplasmic reticulum calcium ion transport
intersection_of: GO:0006816 ! calcium ion transport
intersection_of: results_in_transport_involving GO:0016529 ! sarcoplasmic reticulum
[Term]
id: GO:0000066 ! mitochondrial ornithine transport
intersection_of: GO:0015822 ! ornithine transport
intersection_of: results_in_transport_involving GO:0005739 ! mitochondrion


  • SUGGESTED TO_DO: Change to 'results_in_transport_to_from_or_in'. 'involved_in' is ambiguous as to whether it's the organelle/complex that is BEING transported, or if it's a complex/molecule that is being transported TO/FROM/WITHIN the organelle.


  • Eg. the definition for 'endosome transport ; GO:0016197' is:
    • The directed movement of substances into, out of or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
    • Needs to be changed to 'endosomal transport' based on definition. (DONE- MAY 31st 2012)

results_in_transport_along (8 occurences)

  • All look ok- involve movement along filaments/microtubules


results_in_transport_across (7 occurences)

[Term]
id: GO:0034219 ! carbohydrate transmembrane transport
intersection_of: GO:0008643 ! carbohydrate transport
intersection_of: results_in_transport_across GO:0016020 ! membrane
[Term]
id: GO:0034220 ! ion transmembrane transport
intersection_of: GO:0006811 ! ion transport
intersection_of: results_in_transport_across GO:0016020 ! membrane
[Term]
id: GO:0055085 ! transmembrane transport
intersection_of: GO:0006810 ! transport
intersection_of: results_in_transport_across GO:0016020 ! membrane
[Term]
id: GO:0034486 ! vacuolar transmembrane transport
intersection_of: GO:0055085 ! transmembrane transport
intersection_of: results_in_transport_across GO:0005774 ! vacuolar membrane
[Term]
id: GO:0034487 ! vacuolar amino acid transmembrane transport
intersection_of: GO:0006865 ! amino acid transport
intersection_of: results_in_transport_across GO:0005774 ! vacuolar membrane
[Term]
id: GO:0034755 ! iron ion transmembrane transport
intersection_of: GO:0006826 ! iron ion transport
intersection_of: results_in_transport_across GO:0016020 ! membrane
  • The chemical ones should be changed to intersections involving CHEBI terms, and moved to be in the go_chebi_xp file.
E.g. SUGGESTION FOR NEW XP:
[Term]
id: GO:0034219 ! carbohydrate transmembrane transport
intersection_of: GO:0055085 ! transmembrane transport
intersection_of: has_input CHEBI:16646 ! carbohydrate
  • Q: Should the intra-GO ones (E.g. vacuolar transmembrane transport) stay as they are?


results_in_transport_to_from_or_in (1 occurence)

!!! moved from unvetted and change relation - CJM -2009-12-21 [Term] id: GO:0006839 ! mitochondrial transport intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_to_from_or_in GO:0005739 ! mitochondrion

  • Several of the 'results_in_transport_involving' XPs should be moved into this section (see above).