Weekly curation report

[Daniela Digles]

Dear all,

 

here is my report for the curation week.

 

There were 103 pathways with changes. I updated all the featured and approved tags for the pathways with changes.

 

With https://www.wikipathways.org/index.php/Pathway:WP5074 I saw a some strange symbols (e.g. â TM €), which are there already in the first version of this pathway. Can this be intended, or is there something wrong with the font?

 

Egon, in https://www.wikipathways.org/index.php/Pathway:WP4705 you changed dsRNA to type Rna, but others like mRNA and rRNA, and also dsDNA are still classified as metabolites. Is this intended?

 

I found some meta-pathways which are just a list of genes. https://www.wikipathways.org/index.php/Pathway:WP209, https://www.wikipathways.org/index.php/Pathway:WP372

I added the “annotated lists” tag for them. But the note in the pathway mentions it is “only present for statistical purpose”. Are these still useful nowadays?

 

https://www.wikipathways.org/index.php/Pathway:WP2603 is an approved pathway, but contains a long list of entities “to be integrated into pathway”. I’m not an expert on flower biology, but maybe somebody wants to adopt this. I’ve added a needs work tag describing this.

 

In https://www.wikipathways.org/index.php/Pathway:WP3857 the bibliography contains many symbols. Is there an easy way to fix this?

 

Pathways under construction:

https://www.wikipathways.org/index.php/Pathway:WP5023, https://www.wikipathways.org/index.php/Pathway:WP5025 and https://www.wikipathways.org/index.php/Pathway:WP5024  have an under construction tag with “This pathway is under review and not complete. PMIDs for specific interactions have been added as labels to facilitate review. PMIDs will be formatted as literature references once the review is complete.” Is anyone aware if this is already finished? There was a change of “moved PMID of the interactions to full references”, and I don’t see any labels with the interactions (at least from the webpage). Can the construction tag be removed?

 

Marvin, is https://www.wikipathways.org/index.php/Pathway:WP5035 still under construction?

 

I skipped the rest of the > 30 pathways under construction for time reasons.

 

https://www.wikipathways.org/index.php/Pathway:WP5078 contains “(TEST)” in the description, but is not tagged as a test pathway. Does someone know the author (DanaMustafa)?

 

I also skipped the 79 outdated featured version tags, but I already updated several while checking the changed pathways.

 

Search works fine.

 

Freddie is curating next.

 

Best regards,

Daniela

 

 

 

[Egon Willighagen]

On Sun, Jun 13, 2021 at 6:09 PM Daniela Digles <daniela...@univie.ac.at> wrote:

Egon, in https://www.wikipathways.org/index.php/Pathway:WP4705 you changed dsRNA to type Rna, but others like mRNA and rRNA, and also dsDNA are still classified as metabolites. Is this intended?

No, that's not intentional. I guess those did not trigger a test fail, or one that I did not notice.

At this moment it's not easy yet to get all warnings for a single pathway (only for the COVID19 pathways [0]). This is on our todo list.

Egon

0.https://wikipathways.github.io/SARS-CoV-2-WikiPathways/

--

Have you heard about Wikidata already? "Use Scholia and Wikidata to find scientific literature" is a new tutorial from my colleague Lauren Dupuis. https://laurendupuis.github.io/Scholia_tutorial/

-----

E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen

[Kristina Hanspers]

On Sun, Jun 13, 2021 at 9:09 AM Daniela Digles <daniela...@univie.ac.at> wrote:

Pathways under construction:

https://www.wikipathways.org/index.php/Pathway:WP5023, https://www.wikipathways.org/index.php/Pathway:WP5025 and https://www.wikipathways.org/index.php/Pathway:WP5024  have an under construction tag with “This pathway is under review and not complete. PMIDs for specific interactions have been added as labels to facilitate review. PMIDs will be formatted as literature references once the review is complete.” Is anyone aware if this is already finished? There was a change of “moved PMID of the interactions to full references”, and I don’t see any labels with the interactions (at least from the webpage). Can the construction tag be removed?

Thanks Daniela. These were indeed updated by the original author and I just added ontology tags, removed the Under Construction tag and added Approved tag. 

Kristina

[Alex Pico]

Great report!

I fixed the “strange symbols” and other character encoding and protein state issues with https://www.wikipathways.org/index.php/Pathway:WP5074.  Still some odd, non-standard things in this pathway that make it hard to fully understand, but it’s much better now.

 - Alex

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