evidence used in automatic assertion

[pnrobinson]

I see this phrase used in pages like the phenotypes page of http://beta.monarchinitiative.org/disease/OMIM:609311 I do not think the phrase conveys any processable information (I am not sure what it means but I think we are trying to say something like "inferred from electronic annotation" - to use GO speak). Perhaps we should also use this evidence code here?

[nlwashington]

FYI, the data backing this is built on evidence codes from the Evidence Code Ontology, which are rooted in the GO evidence codes.

"IEA" in GO-speak translates to:

[Term]
id: ECO:0000501
name: evidence used in automatic assertion
def: "A type of evidence that is used in an automatic assertion." [ECO:cjm]
subset: valid_with_gene
subset: valid_with_protein
subset: valid_with_protein_complex
synonym: "IEA" EXACT [GOECO:IEA]
synonym: "inferred from electronic annotation" EXACT [GOECO:IEA]
xref: GO_REF:0000004 "Gene Ontology annotation based on Swiss-Prot keyword mapping."
xref: GO_REF:0000023 "Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping."
xref: GOECO:IEA "inferred from electronic annotation"
is_a: ECO:0000000 {is_inferred="true"} ! evidence
intersection_of: ECO:0000000 ! evidence
intersection_of: used_in ECO:0000203 ! automatic assertion
relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion
created_by: cjm

From the hpo data, if there are records that come in with the string "IEA", I map them to ECO:0000501 (there are a couple of others that i can't, but use another term in the mean time #114).

Perhaps there should be a new label for this term (which I totally support). If the evidence code ontology is not satisfactory for this, @cmungall may have some recommendations.

[pnrobinson]

I think it would be better to show the abbreviation IEA, because showing the entire string "evidence used in automatic assertion" basically means that our Website is implying the user should understand it. Showing IEA, maybe with a link to a details page, means that we think it is a detail that you do not need to understand unless you really want to! -Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

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Von: Nicole Washington [notifications@github.com] Gesendet: Montag, 3. August 2015 09:14 An: monarch-initiative/dipper Cc: Robinson, Peter Betreff: Re: [dipper] evidence used in automatic assertion (#177)

FYI, the data backing this is built on evidence codes from the Evidence Code Ontology, which are rooted in the GO evidence codes.

"IEA" in GO-speak translates to:

[Term] id: ECO:0000501 name: evidence used in automatic assertion def: "A type of evidence that is used in an automatic assertion." [ECO:cjm] subset: valid_with_gene subset: valid_with_protein subset: valid_with_protein_complex synonym: "IEA" EXACT [GOECO:IEA] synonym: "inferred from electronic annotation" EXACT [GOECO:IEA] xref: GO_REF:0000004 "Gene Ontology annotation based on Swiss-Prot keyword mapping." xref: GO_REF:0000023 "Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping." xref: GOECO:IEA "inferred from electronic annotation" is_a: ECO:0000000 {is_inferred="true"} ! evidence intersection_of: ECO:0000000 ! evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: cjm

From the hpo data, if there are records that come in with the string "IEA", I map them to ECO:0000501 (there are a couple of others that i can't, but use another term in the mean time #114https://github.com/monarch-initiative/dipper/issues/114).

Perhaps there should be a new label for this term (which I totally support). If the evidence code ontology is not satisfactory for this, @cmungallhttps://github.com/cmungall may have some recommendations.

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/dipper/issues/177#issuecomment-127145702.

[nlwashington]

@cmungall shall we try to use abbreviations as the preferred item to put into GOLR as the label for any ECO code?

[nlwashington]

moving this issue to downstream where it can be tackled.

[kshefchek]

passing it back, https://github.com/SciGraph/golr-loader/issues/11