GOCHE meeting 2011-11-09

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CHEBI-GO Meeting

Wednesday 9th November 2011

UCL

Present from GO:

  • David Hill
  • Tanya Berardini
  • Jane Lomax
  • Chris Mungall
  • Heiko Dietze
  • Peter D'Eustachio
  • Rebecca Foulger
  • Paola Roncaglia
  • Harold Drabkin (via skype)

Present from ChEBI:

  • Paula DeMatos
  • Gareth Owen
  • Marcus Ennis


Conjugate Acids and Bases

  • GO is inconsistent in its inconsistencies as to whether it represents conjugate acids or bases. Biologists are also inconsistent, and to a point don't really mind which conjugate form their chemical is in. The original plan was to use either the base or the acid in GO term names (citric acid/citrate), but link to the conjugate base in ChEBI. However, Marcus (amongst others) was uncomfortable with this, so other options were discussed:
  • Paula suggested picking pH7.3 and going with the state of the base/acid at that pH. But Peter D'E remarked that different organisms have different pH preferences and different organs work at different pHs, though pH 7.3 works well as a default value.
  • AI: We will go with Chris's suggestion of creating a new relationship, R, where you are talking about the conjugate base OR the conjugate acid. For example for the GO term 'citric acid metabolism', this term will refer to the ChEBI terms 'citrate(1-)', 'citric acid' and 'citrate(2-)', 'citrate(3-).'

[GO citric acid]= [ChEBI Citric acid] U [ChEBI citrate(1-)] U [ChEBI citrate(2-)] U [ChEBI citrate(3-)]. [ChEBI Citric acid], [ChEBI citrate(1-)],[ChEBI citrate(2-)], [ChEBI citrate(3-)] are all related through is_conjugate_acid/is_conjugate_base relationships.

  • AI: We need to standardize the names in GO terms over time, so we don't have the existing inconsistencies:
citrate transport
--[isa]citric acid secretion

* AI: Add related synonyms to all GO terms containing conjugate acids/bases.


* AI: GO does not have to request the conjugate bases for all acids, since the acids and bases will be considered a single type from the GO perspective

Monoamines

  • Are monoamines a role or a structure? David thought that these only had role parents, not structure parents in ChEBI.

In CHEBI, they only have a role parent, but David suggests they should also have a structure. ChEBI outlined how these would be handled in the future by having a chemical with has_role.


Phosphorylated Derivatives

  • Row 165 of the spreadsheet: Why isn't 2-deoxyribose phosphate a pentose in ChEBI? (based on the logic that glucose-6-P is_a hexose)
  • Marcus and Gareth think that glucose-6-P should NOT be a hexose, and that hexose should only refer to the unmodified hexose.

It turns out that GOCHE has:

hexose
--[isa]hexose-phosphate

but CHEBI does NOT have this is_a link (CHEBI has removed this link recently). Therefore GOCHE needs updating accordingly.

  • AI: Create hexose derivative, carbohydrate derivative etc etc terms.
  • David: To make it more complicated, glucose is transported as glucose-6-P: E.g. we've shoe-horned in the biology to the chemical representation.
  • Chris: Confirmed that you are still transporting glucose in this case (if you're transporting something, you're transporting its parts), but it only really works if you have the HAS_PART relationships.
  • Peter: The distinction between glucose and glucose-6-P is critical. In human metabolism, glucose, not glucose-6-P, is the molecule that is transported: the phosphorylated form has no access to the transporter. Indeed, that's how glucose, once taken up into a cell by facilitated diffusion down a concentration gradient, can be stably retained there even if extracellular glucose concentration falls. The whole transport process into a cell involves glucose transport followed by phosphorylation to yield glucose-6-P (a ubiquitous process); export (restricted to a few cell types) requires hydrolysis of intracellular glucose-6-P followed by transport of the glucose out of the cell.

The current GO relationship is wrong:

glucose transport ; GO:0015758
--[isa] glucose 6-phosphate transport ; GO:

has functional parent….. a ChEBI explanation by Gareth, to confused non-chemists

  • ethyl acetate has functional parent: acetic acid
  • Therefore, it means a derivative in the chemical structure sense, rather than can it be made from…


nucleobases, nucleotides, nucleosides

  • We didn't want nucleotides and nucleosides to be carbohydrates in GO. Originally we thought HAS_PART would solve these problems, but this idea has now been scrapped. The more recent idea is that ChEBI will change their structure to instead reflect it with 'has functional parent'.
  • D&T have done work in GO, so that in GO there is now:
nucleobase-containing compound metabolism 
--nucleoside metabolism
--nucleotide metabolism
  • If we're not using HAS_PART, we will need to revisit how these x-containing terms are named.
  • ChEBI has 'nucleobase-containing molecular entity'. which is equivalent to GO's 'nucleobase-containing compound'. ChEBI will stick with the plurals (eg phenols) and add synonyms to the GO term names. GO will do vice-versa.
  • This is the example given in the paper, so we need to work it out in both ChEBI and GO.
  • AI: D&T to work through the nucleobase, nucleoside, nucleotide names in GO to be consistent with ChEBI.

*AI: CHEBI: Change carbohydrate parentage for nucleobases, nucleosides and nucleotides.

  • JANE HAS TAKEN A PICTURE OF THE HAS_FUNCTIONAL PARENT PROPOSAL WRITTEN ON THE BOARD....

[1]

  • Will handle glycoproteins, glycolipids etc in the same way.

base J

  • This is not nucleobase metabolism: this is metabolism that's occurring in a DNA molecule. So base J metabolism would be part_of DNA metabolism.

* AI: Make new term: nucleic acid RESIDUE metabolism : GO:NEW

carnitine CHEBI:17126

  • D&T wanted carnitine to be an amino acid anion, but in ChEBI it's charged neutral.
  • AI: CHEBI to look at this issue.

CHEBI submission Tool

  • Use default, and put in specific terms as comments and leave ChEBI to fix it.


GOCHE Paper

  • Requires minor revisions to work out nucleotide stuff and David will send it round in next week or two.