summary of august sprint for reporting

[raynamharris]

an issue for collecting stats to report for august content generation sprint

[raynamharris]

number of compounds annotated (on staging): 73,498

number of compounds with markdown for LINCS, PubChem, Glygen, and/or DrugCentral

[raynamharris]

contributors: 11?

• data/code/links: rene, mano, sumana, daniel, jeremy yang
• tech support: karl, mike, rayna, jessica, arthur, titus

[raynamharris]

2 relevant videos made for the council of councils meeting

https://nih-cfde.github.io/2022-CoC-Videos/#5-cfde-search-portal-knowledge-base

[raynamharris]

not quite assembled yet, but once it is, there should be new annotations for 17, 985 genes. Annotations include
links to the LINCS reverse search appyter, a knowledge graph, metabolics information, and associated diseases. here's a table of how many genes have each annotation.

[raynamharris]

See also https://hackmd.io/v3cscLr_Qx2tK0WkOeDLaQ?view

[raynamharris]

total number of annotations (used find . -maxdepth 1 -name "*md" | wc -l)

Anatomy

• 321 Embl links
• 50 GTEx widgets
• 19 Knowledge graph links

Compounds

• 33754 Glycan links
• 20638 PubChem links
• 4102 Knowledge Graph links
• 3602 DrugCentral Links

Disease

• 1872 external links
• 479 gene links
• 480 protein links

Genes

• 19971 Appyter links
• 19829 aliases and links
• 19352 GTEx expression widgets
• 19352 transcript widgets
• 17647 knowledge graph links
• 1202 MetGene widgets
• 742 disease page links
• 8 UCSD widgets

Proteins

• 64147 RefSeq links
• 10269 Disease links

[raynamharris]

new overlap, gtex expression widget added to lots of gtex pages

[raynamharris]

resources refreshed on production on Friday, August 26

see #59 for a list of links to specific pages for review

[raynamharris]

the # of resources with markdown content out of total resources in production

• anatomy: 320 of 334
• disease: 1872 of 1894
• compound: 45898 of 73498
• gene: 19962 of 19975
• protein: 64145 of 64145

[raynamharris]

for the announcements nih-cfde/announcements#242

The CFDE Coordinating Center hosted two sprints in July and August to annotate the anatomy, compound, disease, gene, and protein pages in the CFDE Portal to create a knowledge base of information. Thanks to participation from Glycosciences, IDG, LINCS, Metabolomics Workbench, and SPARC, we are excited to announce that we have annotated over 300 anatomies, 1800 diseases, 45000 compounds, 19000 genes, and 64000 proteins. Annotations include images, interactive widgets, aliases, associations, and links to databases. These features are listed under the “Resource” section of each portal page. Here are links to a few representative pages.

• AGRP (gene): https://app.nih-cfde.org/chaise/record/#1/CFDE:gene/id=ENSG00000159723
• AGRP (protein): https://app.nih-cfde.org/chaise/record/#1/CFDE:protein/id=O00253
• L-Glucose (compound): https://app.nih-cfde.org/chaise/record/#1/CFDE:compound/id=10954115
• Obesity (disease): https://app.nih-cfde.org/chaise/record/#1/CFDE:disease/id=DOID%3A9970
• Pituitary Gland (anatomy): https://app.nih-cfde.org/chaise/record/#1/CFDE:anatomy/id=UBERON%3A0000007

[raynamharris]

other examples

GTEx expression data on an anatomy page:
https://app.nih-cfde.org/chaise/record/#1/CFDE:anatomy/id=UBERON%3A0000007
Compound information and visualization:
https://app.nih-cfde.org/chaise/record/#1/CFDE:compound/id=G99997WS
Links to the knowledge graph on compound page:
https://app.nih-cfde.org/chaise/record/#1/CFDE:compound/id=10000456
MANY links and visualization and Appyters on a gene page:
https://app.nih-cfde.org/chaise/record/#1/CFDE:gene/id=ENSG00000000003
Integration of genes with Metabolomics and LINCS on a gene page:
https://app.nih-cfde.org/chaise/record/#1/CFDE:gene/id=ENSG00000000419

[raynamharris]

closed. see https://github.com/nih-cfde/deliverables/pull/423