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nih-cfde / update-content-registry

Code and workflows for adding content to the content registry.
https://app-staging.nih-cfde.org/
BSD 3-Clause "New" or "Revised" License
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list of iframes and links currently in use #64

Open raynamharris opened 2 years ago

raynamharris commented 2 years ago

Links and iframes for security review. See also #59 for links to representative portal pages for review

Anatomy examples

https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0003714 
https://maayanlab.cloud/gene-kg?start=Cell+or+Tissue+%28HuBMAP%29&start_field=id&start_term=UBERON_0002108

::: iframe [**Expression data from GTEx:**](https://mii.podvis.org/cfde-ge1/#/anatomy?uberon_ids=UBERON%3A0004550&width=1400&height=550&numTopGenes=25){width="1400" height="550" style="border: 1px solid black;" caption-style="font-size: 24px;" caption-link="https://gtexportal.org/home/api-docs/index.html#/expression" caption-target="_blank"} 
:::

Compound examples

https://pubchem.ncbi.nlm.nih.gov/compound/91851962 
https://www.glygen.org/glycan/G99997WS
https://maayanlab.cloud/gene-kg?start=Drug&start_field=id&start_term=CID%3A9989505
https://drugcentral.org/drugcard/2493

![Image](https://api.glygen.org/glycan/image/G99997WS)
![DrugCentral Image](https://drugcentral.org/drug/2493/image)

Disease examples

https://disease-ontology.org/?id=DOID:9993
https://bioportal.bioontology.org/ontologies/DOID?p=classes&conceptid=DOID:9993
https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=DOID:9993
https://www.yeastgenome.org/disease/DOID:9993

https://app.nih-cfde.org/chaise/record/#1/CFDE:gene/id=ENSG00000141646
https://app.nih-cfde.org/chaise/record/#1/CFDE:protein/id=O75197

Gene examples

http://www.ensembl.org/id/ENSG00000288611
https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4522
https://www.ncbi.nlm.nih.gov/gene/2831
https://omim.org/entry/600730
https://view.ncbi.nlm.nih.gov/protein/NM_005285
https://www.uniprot.org/uniprot/H9NIL7

https://appyters.maayanlab.cloud/CFDE-Gene-Partnership/#?args.gene=ENSG00000289604&submit
https://appyters.maayanlab.cloud/Gene_Centric_GEO_Reverse_Search/#?args.species_input=Human&args.human_gene=CTAGE8&submit
https://maayanlab.cloud/gene-kg?start=Gene&start_field=label&start_term=CTAGE8

https://app.nih-cfde.org/chaise/record/#1/CFDE:disease/id=DOID%3A10283

https://bdcw.org/MetGENE/index.php?species=hsa&GeneIDType=ENSEMBL&GeneInfoStr=ENSG00000288362&anatomy=NA&disease=NA&phenotype=NA

::: iframe [**Gene-centric Metabolomics Information Retrieval Tool (via MetGene API): ENSG00000288362**](https://bdcw.org/MetGENE/mgSummary.php?species=hsa&ENSEMBL=ENSG00000288362&viewType=all){width="1200" height="350" style="border: 1px solid black;" caption-style="font-size: 24px;" caption-link="https://bdcw.org/MetGENE/index.php?species=hsa&GeneIDType=ENSEMBL&GeneInfoStr=ENSG00000288362&anatomy=NA&disease=NA&phenotype=NA" caption-target="_blank"} 
:::

::: iframe [**Expression data (via GTEx API):**](https://mii.podvis.org/cfde-ge1/#/gene_tissues?gencode_id=ENSG00000284546&width=1200&height=450&numTopTissues=10){width="1200" height="450" style="border: 1px solid black;" caption-style="font-size: 24px;" caption-link="https://gtexportal.org/home/api-docs/index.html#/expression" caption-target="_blank"} 
:::

::: iframe [**LINCS Chemical Perturbations (via LINCS API):**](https://lincs-reverse-search-dashboard.dev.maayanlab.cloud/#CTAGE8){width="1200" height="450" style="border: 1px solid black;" caption-style="font-size: 24px;" caption-link="https://lincs-reverse-search-dashboard.dev.maayanlab.cloud/#CTAGE8" caption-target="_blank"} 
:::

::: iframe [**Transcript list (via GTEx API):**](https://mii.podvis.org/cfde-ge1/#/gene_transcripts?gencode_id=ENSG00000284546&width=1200&height=300){width="1200" height="300" style="border: 1px solid black;" caption-style="font-size: 24px;" caption-link="https://gtexportal.org/home/api-docs/index.html#/reference" caption-target="_blank"} 
:::

::: iframe [**Context view (via UCSC Genome Browser):**](https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chrX%3A2691187-2741309){width="1200" height="900" style="border: 1px solid black;" caption-style="font-size: 24px;" caption-link="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chrX%3A2691187-2741309" caption-target="_blank"} 
:::

Protein examples

https://www.glygen.org/protein/Z4YNJ9
https://www.uniprot.org/uniprotkb/Z4YNJ9/entry
https://app.nih-cfde.org/chaise/record/#1/CFDE:disease/id=DOID%3A0060577
raynamharris commented 2 years ago

cc @rpwagner