Weekly Announcements to post 01-25-2021

[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.

[abhijna]

Anatomy Working Group Update

At the first CFDE Anatomy Working Group (cAWG) meeting GTEx and LINCS explained what their datatypes are and how they describe them. They are working towards a shared understanding of what types of anatomy the CFDE needs to support as well as at what level. GTEx has data at both gross and micro anatomy levels, and has biosamples, images, and bioinformatic data like RNAseq. LINCS has data and metadata terms and standards for cell lines, as well as tools to help query and visualize anatomical locations from which these cell lines were derived. LINCS plans to provide answers to questions about the granularity of search queries and others in following cAWG meetings.

You can check out the cAWG Agenda for meeting notes and information on communicating with or joining the group.

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held on Jan 19, 2021, members decided on a regular meeting time (~3 Eastern on Tuesdays), and heard presentations by two common fund programs: GTEx and LINCS.

GTEx: Their primary need is to sample the same anatomical site reliably and repeatedly. They have good existing standard operating procedures (SOPs) but they still see tissue sample heterogeneity based on RNAseq. GTEx is willing to share its SOPs, and coordinate with other common fund programs to standardize the procedure. The most common search case is "gene of interest" search to look for expression level by tissue. Extensive visualization for tissue-specific expression and sampling locations are available through the GTEx portal. GTEx has begun the process of mapping with Uberon IDs, and their portal can already input a tissue name and return tissue ID.

LINCS: They study how different cell lines respond to stressors using a library of signatures of drugs, small molecules, antibodies, genetic/microenvironment perturbations. They have a variety of tools that support anatomy terms like Slicr for gene expression, LINCS tool marketplace, Clue.io, and the clue cell app. LINCS annotates its cell lines according to the Cell Line Ontology (CLO) scheme. They have over 130 tissues/organs, and all metadata standards are provided on the lincsprojects.org website. Search for an anatomical component on the LINCS portal should return available matching cell lines. The L1000FWD facilitates complex queries and provides cell-type-specific maps, as well as coloring by cell line of the global map. All cell lines are annotated with CLO, ATCC number & disease association, and other metadata is collected from each bio-sample. Moreover, this information can be encoded as a rubric in FAIRshake to evaluate compliance (FAIRness). LINCS will provide answers to questions about the granularity of search queries and others in the following cAWG meetings.

[jeremywalter]

Welcome

CFDE-CC: David Kelly

[jeremywalter]

CFDE Announcements

Greetings CFDE Members! To finish an eventful January we share Cross-Pollination and Training updates and report on the kick-off meeting of our new CFDE Anatomy Working Group (cAWG).

Cross-Pollination Events

The CFDE Cross-Pollination Series continues next week on Tuesday, February 2, at 11am(PST)/2pm(EST). Cross-Pollination events take place on the first Tuesday of every month. LINCS, SPARC, and the NIH are our scheduled presenters. Please check out the Cross-Pollination Schedule and let us know if you would like to present! When requesting a slot please include your preferred date and the length of your talk. Currently we have speakers scheduled out through June, but you can book a slot from July onwards.

In February and March we are adding two new Cross-Pollination Events on Tuesday, February 16 and March 16. These 1.5 hour events will introduce the new R03 awards and share their projects and progress in the CFDE.

Working Groups

Anatomy Working Group Update

At the first CFDE Anatomy Working Group (cAWG) meeting GTEx and LINCS explained what their datatypes are and how they describe them. They are working towards a shared understanding of what types of anatomy the CFDE needs to support as well as at what level. GTEx has data at both gross and micro anatomy levels, and has biosamples, images, and bioinformatic data like RNAseq. LINCS has data and metadata terms and standards for cell lines, as well as tools to help query and visualize anatomical locations from which these cell lines were derived. LINCS plans to provide answers to questions about the granularity of search queries and others in following cAWG meetings.

You can check out the cAWG Agenda for meeting notes and information on communicating with or joining the group.

Ontology Working Group Update

The Ontology Working Group has scheduled their inagaural meeting on February 3 at 8am(PST)/11am(EST). You can get involved by joining their mailing list and slack channel.

CFDE Trainings and Workshops

Pilot workshops are coming up on topics such as Cloud-Compute, Data Resource Training, and Bioinformatics. Our next training will take place on January 29 at 11am(PST)/2pm(EST). This workshop will provide an introduction to Amazon Web Services.

On February 11, at 10am(PST)/1pm(EST) we will have a session on how to use the Kids First Data Resource Portal: Kids First Portal Training Registration.

Welcome

CFDE-CC: David Kelly

Contributing

You can contribute to the next announcements by commenting on the open announcements issue in this repository.

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

Jeremy Walter

CFDE Coordination Team