Curation report - search not showing latest pathways

[Daniela Digles]

Hi,

 

here is my curation report for the week:

24 recently changed pathways.

Some questions/issues:

- On WP3888 I saw that several Publications were having a Pubmed ID, but no Author list and Title. Is there an easy way to fix this issue? Also, the description has individual references, and at least some of them are not included in the Bibliography. Should they also be there, or is it fine to have them in the description only?

- How do you usually welcome new users if their first pathway already looks very advanced? I feel strange welcoming them with the standard “If you need any help”-message. E.g. for WP5060

 

Not much else to report, except for the search, which does not seem to work properly:

 

I searched for the latest pathway: https://www.wikipathways.org/index.php/Special:SearchPathways?query=FOXP3+in+COVID-19&doSearch=1 but it is not included in the results (should be WP5063)

 

The search https://www.wikipathways.org//index.php?query=peptidoglycan+cytoplasmic&species=Escherichia+coli&title=Special%3ASearchPathways&doSearch=1&ids=&codes=&type=query  finds an “Image does not exist”, the link leads to a missing pathway https://www.wikipathways.org/index.php/Pathway:WP5059

 

Next one is Friederike!

 

Best regards,

Daniela

 

 

 

[Martina Summer-Kutmon]

Thanks, Daniela!

I'll try to check the indexer tonight.

Best, Tina

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[Friederike Ehrhart]

Dear all,

 here is my curation report for the last week:

Rikki Frederiksen - new pathway without connecting interactions, E. coli pathway but Salmonella, completely unlined ENSIDs - anyone knows this user? any possibility to contact her/him? apart from WP talks/discussion page

Max Saller - also here, best would be to contact directly.

WP5025 - I think he added PMIDs as data nodes, someone explain him how to add references ;)
WP5055 - dont use color filled nodes, change Uniprot-swissprot IDs to uniprot-trembl, PMIDs also
WP5057 - color filled nodes

Joe G. WP5060 - some uniprot-swissprot IDs

WP229, WP4725, WP4153, WP5064 - Denise added Nieman Pick disease node - do you plan to do that to all pathways with that disease gene? why? we have addons/linksets for that ;)

Covid19 people - do we have IDs for S1 and S2? (cleavage products of protein S)

I approved WP4010 - Liver steatosis AOP - Marvin, Ok?

Next: Nhung!

Best regards,

Freddie

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[Kristina Hanspers]

Thanks Freddie!

Comments for a couple of issues:

The salmonella pathway uploaded by Rikki was discussed on the mailing list and is being used for direct mapping without a database/system code, so the upload was expected. I think the plan was to add an entry for the Salmonella to BridgeDb so that it could be selected as a species, without having a database. Database may come later, if there is community interest.

I've been in contact with Max Saller, they had a problem with PubMed search for literature references not working on certain devices (firewall maybe), so that's why they added them as a label. It is now partially fixed so the pathways can be updated. I will follow up with them about this and the other issues you raised about their content.

Thanks,

Kristina

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[Kristina Hanspers]

Hi admin curators,

A clarification on the pathways from Max Saller, that list PMIDs as labels on interactions:

The pathways are part of a systematic review and as such will be reviewed by people outside of the author's group, and outside of PathVisio. So PMIDs were added as labels to interactions to help make the review easier, and once the review is done they will be transferred to proper literature references in the gpml. Its an interesting use case that I don't think we've seen before.

I have added a note about this on the affected pathways (WP5023, WP5024, WP5025) in the "Under Construction" tag. 

Thanks,

Kristina

On Mon, Mar 8, 2021 at 12:28 AM Friederike Ehrhart <friederik...@gmail.com> wrote:

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