[go] evidence code ontology
Chris Mungall
cjm at fruitfly.org
Wed Feb 6 11:21:08 PST 2008
You can make requests on the RO tracker, see:
http://obofoundry.org/ro
Examples and definitions help
It would be great to have TAIR RO-compliant
involved_in would probably be the same as participates_in
Is regulates used in the same sense as GO?
On Feb 6, 2008, at 10:26 AM, Sue Rhee wrote:
> 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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