added EDAM ontology #41
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annefou
commented
Jul 22, 2020
annefou
commented
- Used https://ifb-elixirfr.github.io/edam-browser/ and added EDAM ontology for each Galaxy climate tool.
- Updated contributing guidelines to make sure we don't forget to add EDAM ontologies.
make sure we know that ADAM ontologies need to be added when creating a new tool
tools/psy-maps/psy-maps.xml
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| @@ -212,4 +212,11 @@ psyplot and psy-maps can be found at https://psyplot.readthedocs.io/projects/psy | |||
| ]]></help> | |||
| <citations> | |||
| </citations> | |||
| <edam_topics> | |||
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Hi, the IUC guidelines recommend to put those sections on top: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html?highlight=order#coding-style
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Ooops :(
When we discussed it this winter for the IUC tools @bgruening, I remember you suggested to put it next to the citations (also xrefs), in the order of xrefs, edam_topics, edam_operations, citations. Which is also what I've been following. And I also think that makes sense, having all the IDs/links together. More thoughts?
So change the docs (PR #58), or redo how we've been annotating so far?
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Ok. I moved them at the top... At least it is consistent with the documentation!
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Thanks @matuskalas. Yeah, currently I just stick to IUC guideline. Thanks for bringing up the topic on IUC - the correct place to discuss this!
| - [Physics](https://ifb-elixirfr.github.io/edam-browser/#topic_3318) (topic_3318) | ||
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| We may need to update all the tools later when additional topics will be added for geosciences. | ||
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Would it be useful to also mention that whoever edits this stuff (in Firefox, or maybe also Chrome), can install the EDAM Popovers plugin?
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Excellent idea. I installed firefox on my laptop to get it; I did not managed to install it with chrome. And it is definitely great! Thanks!
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@annefou if you feel like it please add those tipps and instructions to IUC and any other repo that you find :)
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Yes. I'll add an issue in IUC and make a PR. Thanks for your suggestion.
| <edam_operations> | ||
| <edam_operation>operation_2238</edam_operation> | ||
| <edam_operation>operation_3432</edam_operation> | ||
| <edam_operation>operation_0573</edam_operation> |
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This Map drawing concept is unfortunately messy in EDAM, because it's defined only as "DNA" map drawing (Is that an established term?). So TODO for EDAM, to add either a generic or a geographical Map drawing concept, but then also review all the usage of this concept in bio.tools (looks like it will need even more map-creating concepts), Debian, Galaxy, etc. So great to keep using it here for now (🥇@annefou) as a placeholder, but we'll need to update it in the future, when EDAM is improved.
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Yes of course... I did not think about it! For me a map is always a geographical map!!!
| - [Physics](https://ifb-elixirfr.github.io/edam-browser/#topic_3318) (topic_3318) | ||
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| We may need to update all the tools later when additional topics will be added for geosciences. | ||
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Would it be useful to also mention that whoever edits this stuff (in Firefox, or maybe also Chrome), can install the EDAM Popovers plugin?
EDAM section should be at the top after description.
works on firefox (did not work for me on chrome) and it is very useful.
