CFDE Announcements to Post 05-16-2022

[jeremywalter]

Add a comment containing your interesting links and announcements here! Let us know under which heading your post belongs (or add your own): Critical Announcements Events Meeting Outcomes Resources Tools New Releases Welcome/Farewell

*Please let us know if you would like your Announcements to be added to the Cross Pollination mailing list which includes Data Centers not onboarded with the CFDE.

[jeremywalter]

Critical Announcements

The next submission deadline for DCC data is June 15 (need to confirm).

When submitting data, please note that the C2M2 field biosample.assay_type will be renamed to biosample.sample_prep_method, making the new version better-defined and more straightforward to populate. Values will still be drawn from OBI as before, but should now only be drawn from the "planned process" branch, excluding the "assay" subtree. The sample_prep_method field should now be used exclusively to describe the preparation method (if any, & if available) of the biosample to which the field is attached. Null values are allowed. All DCCs are asked to review and repopulate this field according to the new definition: if this is not possible, please remove all values from the field. This is a backward-compatibility-breaking change: supplied values must either be updated or removed prior to resubmission. As always, if OBI does not offer a term suitable for a given sample prep method, please contact Michelle Giglio (mgiglio@som.umaryland.edu) or the CFDE Ontology Working Group for assistance in rapidly securing a temporary term ID from OBI, which can then be used immediately in C2M2 submissions.

[abradyIGS]

Formatting edits follow -- do what you like in terms of re-styling this version however you want for the actual email, but some of the formatting didn't make it over here from JIRA, so I'm putting it back. Recommend at least emphasizing the sentence about this being a backward-compat-breaking change, or there will be an efflorescence of "I didn't know"s in about a month.

---

The C2M2 field biosample.assay_type will be renamed to biosample.sample_prep_method, making the new version better-defined and more straightforward to populate. Values will still be drawn from OBI as before, but should now only be drawn from the "planned process" branch, excluding the "assay" subtree. The sample_prep_method field should now be used exclusively to describe the preparation method (if any, & if available) of the biosample to which the field is attached. Null values are allowed. All DCCs are asked to review and repopulate this field according to the new definition: if this is not possible, please remove all values from the field. This is a backward-compatibility-breaking change: submitted values must either be updated or removed prior to resubmission. As always, if OBI does not offer a term suitable for a given sample prep method, please contact Michelle Giglio (mgiglio@som.umaryland.edu) or the CFDE Ontology Working Group for assistance in rapidly securing a temporary term ID from OBI, which can then be used immediately in C2M2 submissions.

[ctb]

all hands meeting announce info goes here

[AviMaayan]

The LINCS DCIC published a paper in the 2022 webserver issue of Nucleic Acid Research (https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac328/6582159?login=false) describing the SigCom LINCS web portal (https://maayanlab.cloud/sigcom-lincs/#/). SigCom LINCS serves over a million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. It is built with Signature Commons (https://github.com/MaayanLab/signature-commons), a cloud-agnostic skeleton Data Commons with a focus on serving searchable signatures. SigCom LINCS is findable, accessible, interoperable, and reusable (FAIR) with metadata linked to standard ontologies and vocabularies. In addition, all the data and signatures within SigCom LINCS are available via a well-documented API (https://smart-api.info/registry?q=sigcom).

This can be under "Resources" and added to the Cross Pollination mailing list.

[ctb]

FASEB data works - details in helpdesk. The Federation of American Societies for Experimental Biology

FASEB and National Institutes of Health are championing a bold vision of data sharing and reuse. The DataWorks! Prize fuels this vision with an annual challenge that showcases the benefits of research data management while recognizing and rewarding teams whose research demonstrates the power of data sharing and reuse practices to advance scientific discovery and human health.

Share your story and win:

We are seeking new and innovative approaches to data sharing and reuse in biological and biomedical research. The 2022 DataWorks! Prize will distribute up to $500,000 in awards.

https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fclick.icptrack.com%2Ficp%2Frelay.php%3Fr%3D40524122%26msgid%3D389205%26act%3D35CB%26c%3D1433802%26pid%3D955646%26destination%3Dhttp%253A%252F%252Fwww.herox.com%252Fdataworks%26cf%3D6604%26v%3D6b0f294cee7c2f90194a34fd0dd74ee3c9c164baeb31cd692265b1511c46b12b&data=05%7C01%7Chaluk.resat%40nih.gov%7C590f60c97951402974a108da337057aa%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C637878854846540848%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=o5fRCMPp%2Fs1Whz2WnBg66SXyPLiA%2F9KUu23tekeXavY%3D&reserved=0

[jessicalumian]

Disregard @abradyIGS's comment about the portal updates, the correct text is here:

Subject: Upcoming Data Submission Deadline for CFDE Portal

The next data submission deadline for the CFDE Portal will be June 15. All groups who would like to update their data must submit and approve it by this deadline.

If you would not like to update or submit new data, no action is required on your part. Previously submitted data will be included in this data release.

The latest master JSON schema: https://osf.io/c63aw/ The submission script and prep tables: https://osf.io/bq6k9/ Informational wiki: https://github.com/nih-cfde/published-documentation/wiki/C2M2-Table-Summary

Please contact the help desk with any questions at: support@cfde.atlassian.net

[jeremywalter]

CFDE Announcements -- DRAFT

June All-Hands Meeting

The CFDE Program Team is pleased to announce we will be holding the annual CFDE Program Meeting on June 9-10, 2022 at the Bethesdan Hotel in Bethesda, MD. The purpose of this meeting is to bring the CFDE community together to review progress over the past year and discuss strategic issues that impact the ecosystem as a whole. At this time, we are striving for an all in-person meeting. You can find details about the event including travel recommendations and booking links out our 2022 June All-Hands Meeting Website or you can click here to book a hotel room now. Discounted room rates are available until May 20.

Cross-Pollination Events

Our next scheduled meeting will take place June 7th at 11am PT / 2pm ET. Regular Cross-Pollination events take place on the first Tuesday of every month. Please check out the Cross-Pollination Schedule for more details. Please let us know at support@cfde.atlassian.net if you have something to share!

Upcoming Data Submission Deadline for CFDE Portal

The next data submission deadline for the CFDE Portal will be June 15. All groups who would like to update their data must submit and approve it by this deadline. If you would not like to update or submit new data, no action is required on your part. Previously submitted data will be included in this data release.

The latest master JSON schema: https://osf.io/c63aw/ The submission script and prep tables: https://osf.io/bq6k9/ Informational wiki: https://github.com/nih-cfde/published-documentation/wiki/C2M2-Table-Summary

Please contact the help desk with any questions at: support@cfde.atlassian.net

LINCS Publication

The LINCS DCIC published a paper in the 2022 webserver issue of Nucleic Acid Research (https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac328/6582159?login=false) describing the SigCom LINCS web portal (https://maayanlab.cloud/sigcom-lincs/#/). SigCom LINCS serves over a million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. It is built with Signature Commons (https://github.com/MaayanLab/signature-commons), a cloud-agnostic skeleton Data Commons with a focus on serving searchable signatures. SigCom LINCS is findable, accessible, interoperable, and reusable (FAIR) with metadata linked to standard ontologies and vocabularies. In addition, all the data and signatures within SigCom LINCS are available via a well-documented API (https://smart-api.info/registry?q=sigcom).

FASEB DataWorks! Prize

The Federation of American Societies for Experimental Biology (FASEB) the National Institutes of Health are championing a bold vision of data sharing and reuse. The DataWorks! Prize fuels this vision with an annual challenge that showcases the benefits of research data management while recognizing and rewarding teams whose research demonstrates the power of data sharing and reuse practices to advance scientific discovery and human health. They are seeking new and innovative approaches to data sharing and reuse in biological and biomedical research. The 2022 DataWorks! Prize will distribute up to $500,000 in awards.

Working Group Updates

Working Group	Date	Time	Agenda
Anatomy	TBD	9am PT / 12pm ET	Anatomy WG
Gene	TBD	11am PT / 2pm ET	Gene WG
Gene Expression	May 23rd	11am PT / 2pm ET	Gene Expression Data Exchange
Knowledge Graph	May 17th	12pm PT / 3pm ET	Knowledge Graph WG
Ontology	May 18th	8am PT / 11am ET	Ontology WG

Contributing

You can contribute to the next announcements by commenting on the open announcements issue in this repository. Share your events and updates by posting links and descriptions in our announcements issue! If you have questions about these or other events/activities in the CFDE, contact our helpdesk at support@cfde.atlassian.net

Thank you all for your efforts and have a great week!

Jeremy Walter