data.md

 # Source data
 
-The CC capitalizes on many data sources. The following is an extensive list of resources that are worth considering in current and future versions of the CC. Inside each CC level, I list the resources in **alphabetical order**. Some resources may be repeated because some of them have different types of data. 
+The CC capitalizes on many data sources. The following is an extensive list of resources that are worth considering in current and future versions of the CC. Inside each CC level, I list the resources in **alphabetical order**. Please feel free to update the list at any time. 
 
-I recommend visiting the [NAR Online Molecular Biology Database Collection](http://www.oxfordjournals.org/nar/database/c/#) and [OmicsTools](https://omictools.com/) to stay up-to-date with the literature.
+I recommend visiting the [NAR Online Molecular Biology Database Collection](http://www.oxfordjournals.org/nar/database/c/#) and [OmicsTools](https://omictools.com/) to stay up-to-date with data releases. Also, the [LINCS Data Portal](http://lincsportal.ccs.miami.edu) is of interest.
 
 * [X] Already in the CC.
 * [ ] Not yet in the CC.
@@ -44,6 +44,8 @@ I recommend visiting the [NAR Online Molecular Biology Database Collection](http
  * Chemical-target-based assay activity
 * [ ] Comparative Toxicogenomics Database (CTD) [[paper](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky868/5106145) [data](http://ctdbase.org/)]
  * Chemical-gene interaction data, including regulatory interactions
+* [ ] Drug Repositioning Hub [[paper](https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&retmode=ref&cmd=prlinks&id=28388612) [data](https://clue.io/repurposing)]
+ * Drug indications
 * [X] DrugBank [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753335/) [data](https://www.drugbank.ca/)]
  * Known drug targets with pharmacological action
  * Drug metabolizing enzymes
@@ -69,7 +71,7 @@ I recommend visiting the [NAR Online Molecular Biology Database Collection](http
  * Chemical ontology of biological roles
 * [X] InWEB [[paper](https://dx.doi.org/10.1038%2Fnmeth.4083) [data](https://www.intomics.com/inbio/map.html)]
  * Integrative protein interaction database
-* [X] KEGG [[paper](https://academic.oup.com/nar/article/44/D1/D457/2502600) [data](https://www.genome.jp/kegg/)]
+* [X] Kyoto Encyclopedia of Genes and Genomes (KEGG) [[paper](https://academic.oup.com/nar/article/44/D1/D457/2502600) [data](https://www.genome.jp/kegg/)]
  * A standard pathway database
 * [X] MetaPhORS [[paper](https://academic.oup.com/nar/article/39/5/e32/2409505) [data](orthology.phylomedb.org/)]
  * Orthology and paralogy relationships between genes
@@ -85,22 +87,50 @@ I recommend visiting the [NAR Online Molecular Biology Database Collection](http
 
 ### `D` Cells
 
-* [ ] Genomics of Cell Sensitivity in Cancer ([GDSC]())
-* [ ] Cancer Cell Line Enciclopedia ([CCLE]())
-* [ ] Cancer Therapeutic Response Portal (CTRP) [[paper]() [data]()]
- * 
-* [ ]
+* [X] Broad Therapeutics morphology data [[paper](www.pnas.org/content/111/30/10911) [data](http://lincsportal.ccs.miami.edu/datasets/view/LDS-1195)]
+ * 812-feature cell-painting assays
+* [ ] Cancer Therapeutic Response Portal (CTRP) [[paper](https://www.cell.com/cell/fulltext/S0092-8674(13)00960-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867413009604%3Fshowall%3Dtrue) [data](https://portals.broadinstitute.org/ctrp)]
+ * Large cell line panel of drug sensitivity profiles.
+* [X] ChEMBL [[paper](https://academic.oup.com/nar/article/45/D1/D945/2605707) [data](https://www.ebi.ac.uk/chembl/)]
+ * Literature cell-based assays
+* [ ] Clue.io morphology [[data](https://clue.io/morphology)]
+ * Cell painting assay
+* [ ] Genomics of Cell Sensitivity in Cancer (GDSC) [[paper](https://www.cell.com/fulltext/S0092-8674(16)30746-2) [data](https://www.cancerrxgene.org/)]
+ * Large cell line panel of drug sensitivity profiles
+* [X] MOSAIC [[paper](https://academic.oup.com/bioinformatics/article-abstract/34/7/1251/4677256) [data](http://mosaic.cs.umn.edu)]
+ * Chemical-genetic interaction data in yeast
+* [X] Next-Generation L1000 Connectivity Map [[paper](https://www.cell.com/cell/abstract/S0092-8674(17)31309-0) [data](https://clue.io/data)]
+ * Transcriptomics perturbational data
 * [X] NCI-60 [[paper](https://academic.oup.com/jnci/article/108/5/djv388/2412594) [data](https://dtp.cancer.gov/databases_tools/bulk_data.htm)]
  * Cell-line growth-inhibition data
 
 ### `E` Clinics
 
-* [X] 
-
-
-## Prediction tools
-
-
-
+* [X] ChEMBL [[paper](https://academic.oup.com/nar/article/45/D1/D945/2605707) [data](https://www.ebi.ac.uk/chembl/)]
+ * Drug indications
+ * Therapeutic areas
+* [X] Comparative Toxicogenomics Database (CTD) [[paper](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky868/5106145) [data](http://ctdbase.org/)]
+ * Compound-disease associations
+* [ ] Drug Repositioning Hub [[paper](https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&retmode=ref&cmd=prlinks&id=28388612) [data](https://clue.io/repurposing)]
+ * Drug indications
+* [X] DrugBank [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753335/) [data](https://www.drugbank.ca/)]
+ * Drug-drug interactions
+ * Therapeutic areas
+* [ ] DrugCentral [[paper](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky963/5146206) [data](http://drugcentral.org)]
+ * Drug indications
+ * Drug side effects
+* [X] Kyoto Encyclopedia of Genes and Genomes (KEGG) [[paper](https://academic.oup.com/nar/article/44/D1/D457/2502600) [data](https://www.genome.jp/kegg/)]
+ * Therapeutic areas
+* [ ] OFFSIDES [[paper](http://stm.sciencemag.org/content/4/125/125ra31.long) [data](https://www.pharmgkb.org/downloads)]
+ * Side effects
+* [X] Side Effect Resource (SIDER) [[paper](https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1075) [data](sideeffects.embl.de/)]
+ * Drug side effects
+* [X] RepoDB [[paper](https://www.nature.com/articles/sdata201729) [data](apps.chiragjpgroup.org/repoDB/)]
+ * Drug indications
+* [ ] TWOSIDES [[paper](http://stm.sciencemag.org/content/4/125/125ra31.long) [data](https://www.pharmgkb.org/downloads)]
+ * Drug-drug interactions
+
+## Prediction and calculation methods
 
-## 
+* [ ] 
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+* [ ] 
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