Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

bio.tools EDAM #169

Open
wants to merge 5 commits into
base: master
Choose a base branch
from
Open

bio.tools EDAM #169

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
View file
Open in desktop
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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 -->
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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 -->
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Same here, leave Enrichment Analysis but remove annotation

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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>
4 changes: 4 additions & 0 deletions tools/ipo/ipo4retgroup.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -229,4 +229,8 @@ Changelog/News
]]></help>

<expand macro="citation" />

<expand macro="edam_topics"/>
<expand macro="edam_operations"/>
<expand macro="xrefs"/>
</tool>
4 changes: 4 additions & 0 deletions tools/ipo/ipo4xcmsSet.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -252,4 +252,8 @@ Changelog/News
]]></help>

<expand macro="citation" />

<expand macro="edam_topics"/>
<expand macro="edam_operations"/>
<expand macro="xrefs"/>
</tool>
20 changes: 20 additions & 0 deletions tools/ipo/macros.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -89,4 +89,24 @@
<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 -->
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

remove (see other comments)

</edam_topics>
</xml>
<xml name="edam_operations">
<edam_operations>
<edam_operation>operation_3627</edam_operation> <!-- Mass spectra calibration -->
<edam_operation>operation_3215</edam_operation> <!-- Peak detection -->
<edam_operation>operation_2425</edam_operation> <!-- Optimisation and refinement -->
</edam_operations>
</xml>
<xml name="xrefs">
<xrefs>
<xref type="bio.tools">ipo</xref>
<xref type="bio.tools">workflow4metabolomics</xref>
</xrefs>
</xml>
</macros>
4 changes: 4 additions & 0 deletions tools/msnbase_readmsdata/msnbase_readmsdata.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -251,4 +251,8 @@ Changelog/News
]]></help>

<expand macro="citation" />

<expand macro="edam_topics"/>
<expand macro="edam_operations"/>
<expand macro="xrefs"/>
</tool>
12 changes: 12 additions & 0 deletions tools/nmr_annotation/asics_xml.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -222,5 +222,17 @@ Example
<citation type="doi">10.1007/s11306-017-1244-5</citation>
<citation type="doi">10.1093/bioinformatics/btu813</citation>
</citations>
<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_topics>
<edam_operations>
<edam_operation>operation_0226</edam_operation> <!-- Annotation -->
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Would replace with http://edamontology.org/operation_3214 (Spectral analysis) and http://edamontology.org/operation_3799 (Quantification)

</edam_operations>
<xrefs>
<xref type="bio.tools">asics</xref>
<xref type="bio.tools">workflow4metabolomics</xref>
</xrefs>

</tool>
6 changes: 6 additions & 0 deletions tools/xcms_export_samplemetadata/xcms_export_samplemetadata.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -128,4 +128,10 @@ Changelog/News
]]></help>

<expand macro="citation" />

<expand macro="edam_topics"/>
<edam_operations>
<edam_operation>operation_2409</edam_operation> <!-- Data handling -->
</edam_operations>
<expand macro="xrefs"/>
</tool>
6 changes: 6 additions & 0 deletions tools/xcms_fillpeaks/abims_xcms_fillPeaks.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -305,5 +305,11 @@ Changelog/News

<expand macro="citation" />

<expand macro="edam_topics"/>
<edam_operations>
<edam_operation>operation_3557</edam_operation> <!-- Imputation -->
</edam_operations>
<expand macro="xrefs"/>


</tool>
8 changes: 8 additions & 0 deletions tools/xcms_group/abims_xcms_group.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -425,5 +425,13 @@ Changelog/News

<expand macro="citation" />

<expand macro="edam_topics"/>
<edam_operations>
<edam_operation>operation_3628</edam_operation> <!-- Chromatographic alignment -->
<edam_operation>operation_3633</edam_operation> <!-- Retention time prediction -->
<edam_operation>operation_3694</edam_operation> <!-- Mass spectrum visualisation -->
</edam_operations>
<expand macro="xrefs"/>


</tool>
20 changes: 20 additions & 0 deletions tools/xcms_macro/macros_msnbase.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,4 +28,24 @@
<expand macro="citation_w4m"/>
</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_0121</edam_topic> <!-- Proteomics -->
<edam_topic>topic_3307</edam_topic> <!-- Computational biology -->
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

remove

</edam_topics>
</xml>
<xml name="edam_operations">
<edam_operations>
<edam_operation>operation_2409</edam_operation> <!-- Data handling -->
</edam_operations>
</xml>
<xml name="xrefs">
<xrefs>
<xref type="bio.tools">msnbase</xref>
<xref type="bio.tools">workflow4metabolomics</xref>
</xrefs>
</xml>
</macros>
13 changes: 13 additions & 0 deletions tools/xcms_macro/macros_xcms.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -252,4 +252,17 @@ For details and explanations concerning all the parameters and workflow of xcms_
<expand macro="citation_w4m"/>
</citations>
</xml>
<xml name="edam_topics">
<edam_topics>
<edam_topic>topic_2259</edam_topic> <!-- Systems biology -->
<edam_topic>topic_3172</edam_topic> <!-- Metabolomics -->
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

remove

<edam_topic>topic_3307</edam_topic> <!-- Computational biology -->
</edam_topics>
</xml>
<xml name="xrefs">
<xrefs>
<xref type="bio.tools">camera</xref>
<xref type="bio.tools">workflow4metabolomics</xref>
</xrefs>
</xml>
</macros>
6 changes: 6 additions & 0 deletions tools/xcms_merge/xcms_merge.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -198,4 +198,10 @@ Changelog/News
]]></help>

<expand macro="citation" />

<expand macro="edam_topics"/>
<edam_operations>
<edam_operation>operation_3436</edam_operation> <!-- Aggregation -->
</edam_operations>
<expand macro="xrefs"/>
</tool>
6 changes: 6 additions & 0 deletions tools/xcms_plot_chromatogram/xcms_plot_chromatogram.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,4 +116,10 @@ Changelog/News
]]></help>

<expand macro="citation" />

<expand macro="edam_topics"/>
<edam_operations>
<edam_operation>operation_3203</edam_operation> <!-- Chromatogram visualisation -->
</edam_operations>
<expand macro="xrefs"/>
</tool>
7 changes: 7 additions & 0 deletions tools/xcms_retcor/abims_xcms_retcor.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -375,4 +375,11 @@ Changelog/News

<expand macro="citation" />

<expand macro="edam_topics"/>
<edam_operations>
<edam_operation>operation_3628</edam_operation> <!-- Chromatographic alignment -->
<edam_operation>operation_3633</edam_operation> <!-- Retention time prediction -->
</edam_operations>
<expand macro="xrefs"/>

</tool>
5 changes: 5 additions & 0 deletions tools/xcms_summary/abims_xcms_summary.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -128,5 +128,10 @@ Changelog/News


<expand macro="citation" />
<edam_operations>
<edam_operation>operation_0337</edam_operation> <!-- Visualisation -->
</edam_operations>
<expand macro="edam_topics"/>
<expand macro="xrefs"/>

</tool>
7 changes: 7 additions & 0 deletions tools/xcms_xcmsset/abims_xcms_xcmsSet.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -581,4 +581,11 @@ Changelog/News
]]></help>

<expand macro="citation" />

<expand macro="edam_topics"/>
<edam_operations>
<edam_operation>operation_3215</edam_operation> <!-- Peak detection -->
<edam_operation>operation_3860</edam_operation> <!-- Spectrum calculation -->
</edam_operations>
<expand macro="xrefs"/>
</tool>