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bio.tools EDAM #169

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bio.tools EDAM #169

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3ade70c
camera - biotools, edam
lecorguille Jan 21, 2020
2cd106e
ipo - biotools, edam
lecorguille Jan 21, 2020
a667971
msnbase - biotools, edam
lecorguille Jan 21, 2020
cecd1db
asics - biotools, edam
lecorguille Jan 21, 2020
c6b57ad
xcms - biotools, edam
lecorguille Jan 21, 2020
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3 changes: 3 additions & 0 deletions tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -514,5 +514,8 @@ Changelog/News

<expand macro="citation" />

<expand macro="edam_topics"/>
<expand macro="edam_operations"/>
<expand macro="xrefs"/>

</tool>
4 changes: 4 additions & 0 deletions tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
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Expand Up @@ -263,5 +263,9 @@ Changelog/News

<expand macro="citation" />

<expand macro="edam_topics"/>
<expand macro="edam_operations"/>
<expand macro="xrefs"/>


</tool>
19 changes: 19 additions & 0 deletions tools/camera_macro/macros.xml
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Expand Up @@ -165,4 +165,23 @@
<citation type="doi">10.1093/bioinformatics/btu813</citation>
</citations>
</xml>
<xml name="edam_topics">
<edam_topics>
<edam_topic>topic_2259</edam_topic> <!-- Systems biology -->
<edam_topic>topic_3172</edam_topic> <!-- Metabolomics -->
<edam_topic>topic_3307</edam_topic> <!-- Computational biology -->
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I wouldn't include Computational Biology because it is the most generic term. Regarding EDAM annotation, the general rule is that you pick the most specific terms you can, but not their parents

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Any of the other term are children of Computational Biology !?
But I don't know if I can pick a more precise term in Computational Biology ?
If not, I can understand that it should be remove because not enough specific

</edam_topics>
</xml>
<xml name="edam_operations">
<edam_operations>
<edam_operation>operation_0226</edam_operation> <!-- Annotation -->
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Same here, leave Enrichment Analysis but remove annotation

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Enrichment Analysis
Categories from a relevant ontology can be used. The input is typically a set of genes or other biological objects, possibly represented by their identifiers, and the output of the analysis is typically a ranked list of categories, each associated with a statistical metric of over-/under-representation within the studied data.

Annotation
This is a broad concept and is used a placeholder for other, more specific concepts.

Indeed Annotation isn't really specific but so far I don't have anything relevant for metabolomics in this branch. But for me, it's different than discover up or over-/under-metabolomics across samples. Or I misunderstood the "Enrichment Analysis" term :/

<edam_operation>operation_3501</edam_operation> <!-- Enrichment analysis -->
</edam_operations>
</xml>
<xml name="xrefs">
<xrefs>
<xref type="bio.tools">camera</xref>
<xref type="bio.tools">workflow4metabolomics</xref>
</xrefs>
</xml>
</macros>