[go] evidence code ontology
Sue Rhee
rhee at acoma.Stanford.EDU
Wed Feb 6 10:26:22 PST 2008
Yes, I agree that it would be helpful to make any relationships between
ontologies and annotations explicit for many reasons (Hilmar's example
of contradicting evidences for the same assertion is an excellent one).
The following are relationships between GO and genes or between genes
and genes that we have been using in TAIR for ~6 years or so. They
probably should go into the RO, if not there already.
+-------------+-----------------------------------------------+
| annotations | description |
+-------------+-----------------------------------------------+
| 35665 | involved in |
| 563 | functions as |
| 7193 | expressed in |
| 111 | not involved in |
| 181 | not expressed in |
| 401 | related to |
| 72 | required for |
| 6 | not required for |
| 29373 | located in |
| 23 | not located in |
| 222 | is subunit of |
| 222 | constituent of |
| 215 | regulates |
| 10266 | functions in |
| 16 | represses |
| 90 | is regulated by |
| 62 | suppresses gene |
| 46 | enhances gene |
| 3 | partially enhances gene |
| 6 | partially suppresses gene |
| 384 | expressed during |
| 53 | expressed only in |
| 5 | expressed only during |
| 80 | is downregulated by |
| 29784 | has |
| 1237 | has protein-protein physical interaction with |
| 4 | binds to cis-element of |
| 9 | acts upstream of |
| 44 | acts downstream of |
| 27 | has protein-DNA interaction with |
| 437 | has protein modification of type |
| 6 | protein is modified by |
| 57 | does not have |
| 4 | contributes to |
| 35 | colocalizes with |
| 1 | does not function in |
| 355 | is upregulated by |
| 36 | is not regulated by |
| 4 | is not a constituent of |
| 9 | not expressed during |
+-------------+-----------------------------------------------+
Larry Hunter wrote:
>
> Given Sue's comment that
>
>> Perhaps the 'inferred from' should probably be omitted from term
>> names and the ontology renamed as Evidence Source Ontology. In my
>> view, it represents types of methods that are used to generate
>> results that are used as evidences for an assertion. So eventually I
>> see the leaf nodes of this ontology being individual assay types. In
>> this view, the ECO could be considered as some sort of meta ontology
>> for the OBI.
>
> it seems clear that the relation(s) between such evidence sources and
> the propositions (hypotheses? assertions?) that they inform still need
> to be defined, and that these epistemic relations could be used by the
> GO, phenoscape and others to make more explicit the relationship of
> evidence to their annotations.
>
> Currently, the GO makes instance level assertions about genes having a
> particular molecular function, participating in a particular
> biological process, or being located in a particular cellular
> component, and links each such assertion to an evidence code
> (sometimes specifying the PMID of a publication that contains the
> evidence). The instance-level relationship ("has function"
> "participates in" "is located in") is implicit, as is the
> (meta-)relationship between the particular instance level relationship
> and the PMID or other source of evidence.
>
> There may well be value in making these implicit relationships more
> explicit, both for automated reasoning, and for making assertions
> about universals. There are already RO terms (or proposed terms)
> that will make possible explicit instance level statements (e.g.,
> <gene> "participates in" <process>) -- what I am trying to get to is
> the set of relations necessary to make the relationship between such
> statements and the evidence for them explicit. Since all of the GO
> evidence codes (and apparently the ones used by Karp's xCyc systems)
> are related to literature assertions, I am inclined to make the
> definitions in terms of OBI DENRIEs), but more on that in another email.
>
> Larry
>
>
>
>>
>> Sue
>>
>> Suzanna Lewis wrote:
>>> Chris said it much better than I.
>>>
>>> I agree fully with this summary.
>>>
>>> -S
>>>
>>> On Feb 5, 2008, at 4:01 PM, Chris Mungall wrote:
>>>
>>>>
>>>> At the moment, ECO isn't very ontology-like. As Larry pointed out,
>>>> it's more of a terminology of codes with specific instructions on
>>>> what fields should be filled in the GAF. The adoption of ECO by
>>>> phenoscape and the extension to homology-based evidence types is a
>>>> good thing and should hopefully keep ECO general enough for use
>>>> outside GO. At the same time, ECO has to be guaranteed to fulfill
>>>> certain GO requirements.
>>>>
>>>> OBI is a massive and impressive effort - but it is still young. Its
>>>> emphasis is on representing actual experiments and associated
>>>> entities - rather than codes - which is a good thing. It is
>>>> certainly the OBO ontology for representing an experiment. But ECO
>>>> doesn't represent experiments per se - it represents evidence
>>>> and/or inference, which presents additional challenges.
>>>>
>>>> I would say the evidence group should be actively engaging OBI, we
>>>> should be trying to define ECO terms using OBI terms where
>>>> possible. Likewise the OBI group should treat ECO as a set of
>>>> requirements. And I think we can use OBI to provide a better
>>>> structure to ECO. But I think it is too soon to talk of immediately
>>>> subsuming ECO into OBI - sorry Sue, you don't get out of it that
>>>> easily!!
>>>>
>>>>
>>>>
>>>> On Feb 5, 2008, at 3:40 PM, Sue Rhee wrote:
>>>>
>>>>> Hi GO and Phenoscape colleagues,
>>>>>
>>>>> Larry Hunter pointed me to the OBI project
>>>>> (http://obi.sourceforge.net) recently, which I wasn't aware of. It
>>>>> seems to me that the ECO is redundant to and much less developed
>>>>> than the OBI and I would like to suggest that OBI take over
>>>>> merging ECO into their ontology. Please let me know if you have
>>>>> any views on this.
>>>>>
>>>>> Best,
>>>>> Sue
>>>>>
>>>>> --
>>>>> Sue Rhee
>>>>> Staff Scientist
>>>>> Carnegie Institution, Department of Plant Biology
>>>>> 260 Panama Street, Stanford, CA 94305
>>>>> Email: (650) 325-1521 x251
>>>>> Fax: (650) 325-6857
>>>>>
>>>>>
>>>>
>>>>
>>
>> --
>> Sue Rhee
>> Staff Scientist
>> Carnegie Institution, Department of Plant Biology
>> 260 Panama Street, Stanford, CA 94305
>> Email: (650) 325-1521 x251
>> Fax: (650) 325-6857
>>
--
Sue Rhee
Staff Scientist
Carnegie Institution, Department of Plant Biology
260 Panama Street, Stanford, CA 94305
Email: (650) 325-1521 x251
Fax: (650) 325-6857
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