bio.tools EDAM #169
bio.tools EDAM #169
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Oh very cool @lecorguille @sneumann @fgiacomoni !!!! ❤️ |
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It fails but it's the classic IPO tool long jobs. FYI here is the current state-of-art of the workflow4metabolomics bio.tools card : https://bio.tools/workflow4metabolomics |
| <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
| </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_topics> | ||
| <edam_topic>topic_2259</edam_topic> <!-- Systems biology --> | ||
| <edam_topic>topic_3172</edam_topic> <!-- Metabolomics --> | ||
| <edam_topic>topic_3307</edam_topic> <!-- Computational biology --> |
| <edam_topic>topic_3307</edam_topic> <!-- Computational biology --> | ||
| </edam_topics> | ||
| <edam_operations> | ||
| <edam_operation>operation_0226</edam_operation> <!-- Annotation --> |
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Would replace with http://edamontology.org/operation_3214 (Spectral analysis) and http://edamontology.org/operation_3799 (Quantification)
| <edam_topic>topic_2259</edam_topic> <!-- Systems biology --> | ||
| <edam_topic>topic_3172</edam_topic> <!-- Metabolomics --> | ||
| <edam_topic>topic_0121</edam_topic> <!-- Proteomics --> | ||
| <edam_topic>topic_3307</edam_topic> <!-- Computational biology --> |
| <xml name="edam_topics"> | ||
| <edam_topics> | ||
| <edam_topic>topic_2259</edam_topic> <!-- Systems biology --> | ||
| <edam_topic>topic_3172</edam_topic> <!-- Metabolomics --> |
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Is this PR still alive? @lecorguille |
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It would be nice :) Just a small hint, annotating with the bio.tools is enough, no other EDAM annotation is needed as Galaxy tries to get the EDAM mapping directly from bio.tools. |
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+1 for continuing on this @lecorguille @yguitton - happy to contribute if needed! |
Here is a first attempt to annotate the tools.
It take place in the bio.tools hackathon hosted today at Pasteur/Paris
ping @fgiacomoni , @hmenager, @sneumann