GO-CHEBI-Agenda: Difference between revisions

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===Future===
===Future===
#ChEBI next steps - Janna has kept a running list
#ChEBI next steps -  
#*'''Action for CHEBI:''' Janna has kept a running list, she will email to Tanya and Tanya will integrate into wiki
#GO next steps
#GO next steps
#* '''Action for GO:''' use the [https://www.ebi.ac.uk/chebi/submissions/login CHEBI submission tool]to submit everything on Nico's yes list. They will be issued ids immediately. If they're already in CHEBI, they will merge the duplicate entries so the id won't be lost.
#* '''Action for GO:''' use the [https://www.ebi.ac.uk/chebi/submissions/login CHEBI submission tool]to submit everything on Nico's yes list. They will be issued ids immediately. If they're already in CHEBI, they will merge the duplicate entries so the id won't be lost.

Revision as of 17:36, 25 July 2010

Attendees:

Saturday

Background and Introduction

  1. David - Motivation for GOCHE
  2. Chris - how the original GOCHE file was created
  3. David - steps leading up to today
  4. GOALS: GOCHE = CHEBI, improve GO using CHEBI, improve CHEBI using GO
  5. Chris - process of how improvements to GO using CHEBI will be done

Discussion Areas

Derivatives

  1. Discuss clarifying the plural terms in CHEBI, we suspect that the plurals represent what we are calling "X and derivative".
  2. We need a good definition for derivative to use on the '...and derivative' terms Can you help?
  3. Does modified amino acid mean essentially 'amino acid derivative', in which case shouldn't it have an is functional parent relationship with amino acid?
    • Chemists think in terms of chemical skeletons e.g. anything with a phenol aromatic ring is a phenols.
    • Derivatives are entities with common substructures, not necessarily actually derived from one another
    • The substructure also has to be the main component of the derivative.
    • Derivative isn't a very precisely defined term in chemistry

Action for GO: Change `goche id for bezene and derivative for the chebi id for benzenes (uncurated)

  • Can we classify chemicals on the basis of the presence of a substructure, regardless of what the rest of the molecule is?
  • Could CHEBI to rename/define benzenoid aromatic compound to benzene-containing compound, then GOCHE term benzene and derivative can be mapped to this term rather than benzenes? - yes
  • More generally, GOCHE 'x and derivative' terms should be mapped to the 'x-containing compound' parent term rather than the plural

Action for GO: GO to rename the GOCHE 'x and derivative' terms to be 'x-containing compound' throughout

Action for GO: provide CHEBI with a list of the 'x-containing compound' terms for them to add

Conclusion: GOCHE 'x and derivative' terms should be mapped to the 'x-containing compound' (CHEBI will call these 'x-containing molecular entity) parent term rather than the plural. CHEBI will add/rename to create these terms where necessary. These terms will have a has_part relationship to the containing compound.

Macromolecules

  1. Discuss the inclusion of small molecules into Chebi. Could we have macromolecule vs. monomer? How can we make the distinction of what biologists call a 'small molecule'. What is the complement of macromolecule?
    • Meaning of macromolecule in CHEBI to meaning in GOCHE

Conclusion: keep small molecule only in GO - remove from GOCHE. Ensure all children have an alternative structural path.

  1. Protein and its children - some of these in CHEBI. Are they due to be removed? In PRO?
  2. Same for RNAs
    • CHEBI have discussed proteins with PRO - all protein subtypes will move to PRO.
    • Owner of glycoproteins etc yet to be determined. CHEBI might have a term 'protein-chemical complex
    • peptide hormones are just peptides and will live in CHEBI, what is a peptide vs. protein? It is ok if the precursors were encoded by the genome.
    • Action for GO: check through the remaining hormone terms to retain only the peptide hormones, not proteins

Nucleotides, nucleosides etc.

  1. We merged nucleotide and nucleoside phosphate. These seem to be exact synonyms of one another.
    • There are non-naturally occurring nucleoside phosphates that are not nucleotides.
    • Action for GO: when CHEBI has fixed arrangement of nucleoside phosphate/nucleotide, need to fix GOCHE accordingly (can we write formal definitions for this problem and use this example for the paper?)
  2. Purine is not currently is_a purines - is this deliberate or an oversight?
    • An oversight - CHEBI will fix
    • Hypoxantine - should be a purine base in CHEBI?
      Action for GO: Move hypoxanthine up to be a child of 'purine-containing compound' (when we have that term)
  3. Should we merge pyrimidine with pyrimidine (nucleo)base?
    • There is a difference between pyrimidine with pyrimidine (nucleo)base - GOCHE should reflect this
  4. NADH is_a NAD and NADPH is_a NADP. Seems like isa isn't quite right here?
    • Action for GO: GOCHE needs to change NAD to NAD+
  5. Pyridine nucleotide - this looks by its children like it should be a ribonucleotide - should it have this parent/name?
  6. Carbohydrates and nucleotides - should nucleotide have functional parent rather than is_a carbohydrate (N-glycosyl has functional parent carbohydrate)?
    • CHEBI will reorganize these terms using has_part e.g. nucleoside phosphate has_part nucleoside
  7. Created axioms for nucleobase and nucleoside terms. Tagged with GOC:carnegie dbxref. Will pass on to CHEBI and they will do their magic.

Amino acids

  1. Amino acid families - not in CHEBI?
    • We have removed from GOCHE
  2. We need a conjugate base term for 'amino acid'. There may be others. Does CHEBI have a systematic way of checking the conjugate base term is always added?
  3. Relevant files:
    • CHEBI_make_links.txt
    • CHEBI_oxoacids_no_conjugate_base.txt
    • Action for GO: Generate a list of missing conjugate bases for submission to CHEBI. CHEBI will check if the entry already exists, and if it does make the appropriate is_conjugate_base relationship and if not, add it.

Other

  1. mancude organic heterobicyclic parent CHEBI:35570 - should this term really have 'parent' on the end?
    • 48 terms in CHEBI with 'parent' in name.
    • Makes a statement about the role of the representation of the molecule in IUPAC (?)
    • GOCHE should not directly link to these terms
  2. In CHEBI sn-glycerol-3-phosphate is_a glycerol-1-phosphate
    • An oddity due to IUPACs numbering system. GOCHE can ignore. (sn = stereospecifically numbered)
  3. In CHEBI pectin is_a galacturonan. We think this should be petin has_part galacturonan - we've put this in GOCHE
    • CHEBI will fix this. This is one of the cases where the plural was changed to a singular, but in this case wasn't quite correct because pectin is a mixture of polysaccharides.
  4. Is an amide an amine?
    • Two types of amide: only one is an amine so no.
  5. Is 'molybdopterin cofactor' a 'pteridine and derivatives' ?
    • 'molybdopterin cofactor' would be an intersection term in CHEBI, of the role and the structure.
    • Action for GO: Relate this term to the new CHEBI term that refers to the intersection of the CHEBI role and the CHEBI structure
  6. sulfur metabolism = metabolism of S (element) OR sulfur containing compounds, therefore, do we change 'sulfur metabolism' to 'sulfur and sulfur compound metabolism' - sounds like GO 'sulfur' = CHEBI 'sulfur' = 'sulfur and derivative' and GO 'sulfur compound' = ChEBI 'organosulfur compound'
    • CHEBI will change the name of their existing term sulfur molecular entity to term sulfur-containing molecular entity, and add has_part relationship to sulfur.
  7. Is glyoxylate an aldehyde or not?
    • Yes, but GOCHE won't explicitly make it an aldehyde. It will be inferred in a CHEBI relationship.
  8. adrenocorticotropin, prolactin, somatostatin - do these belong in CHEBI or somewhere else?
    • If CHEBI says they are peptides, they will stay under peptides, if not we will put them under proteins and will fall under PRO's scope.
  9. Would CHEBI consider adding small molecule as a counterpart to macromolecule (see GO def)?
    • CHEBI will not add small molecule. GOCHE terms that were children of this term have other parents that trace to chemical already.
  10. What is the relationship between sphingoid and sphingolipid? Is it upside-down?
    • Probably. Will investigate further and fix in CHEBI, if necessary.

Sunday

GOCHE/CHEBI Misalignments

We will make requests on the appropriate SF trackers. We should create a group in ChEBI's tracker for GO requests and a group in GO's tracker for ChEBI. File: go_nojustifiedbyCHEBI (or something like that)

  • Action for GO: sort out the lipoproteins from the lipoprotein particles in GO
  • Action for CHEBI: add a new lipoprotein term for proteins with lipid covalently attached
  • Action for GO: sort out what GO means by phosphate and request appropriate terms from CHEBI
  • Action for GO: rename phenol M,B,C to be phenol-containing compound M, B, C
  • Action for GO: figure out which cobalamin we are talking about? There are several.
  • Action for CHEBI: add retinoic acid, folate, thiamin (others also) as a vitamin
  • Action for CHEBI: magnesium ion need to be metal ion
  • Action for CHEBI: carbohydrate phosphate and children should have_part carbohydrate and have_part phosphate

Edit nucleotide version of CHEBI as Sanity check

Tanya has edited her local copy of chebi. The GO group has checked the paths using metabolism, biosynthesis, catabolism, transport and response to to make sure that this approach works.

nucleotide- works for metabolism, biosynthesis, catabolism, binding and response to.

Tanya has committed this file to CVS. (/go/scratch/obol_results/chebi_nucleotide.obo)

Roles

Colin gave a presentation on his and Janna's work on roles and dispositions. We had a discussion about how these relate to GO. They are interested in this with respect to small molecules. we will want to address this in the paper.

Prosthetic group

Is this a role or not? Yes.

  • Action for GO: - remove 'prosthetic group' from GOCHE

Definition generation

Future

  1. ChEBI next steps -
    • Action for CHEBI: Janna has kept a running list, she will email to Tanya and Tanya will integrate into wiki
  2. GO next steps
    • Action for GO: use the CHEBI submission toolto submit everything on Nico's yes list. They will be issued ids immediately. If they're already in CHEBI, they will merge the duplicate entries so the id won't be lost.
  3. Procedure for future interactions : email, SF trackers, CHEBI submission tool
  4. Need to prevent drift
  5. Create GOCHE-GO xps very soon, will transition to CHEBI