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# Data sources
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.
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, we list the resources in **alphabetical order**. Please feel free to make requests by contacting [](miquel.duran@irbbarcelona.org) or [](patrick.aloy@irbbarcelona.org).
We 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.
In addition, please be aware of the Bioteque project maintained by the SB&NB.
To identify new datasets of your interest, we 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.
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* [X] BindingDB [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702793/) [data](https://www.bindingdb.org/)]. Chemical-protein binding data (patents).
* [X] ChEMBL [[paper](https://academic.oup.com/nar/article/45/D1/D945/2605707) [data](https://www.ebi.ac.uk/chembl/)]. Known drug targets. Drug metabolizing enzymes. Chemical-protein binding. Chemical-target-based assay activity.
* [X] ChEMBL drug target predictor [[blog](http://chembl.blogspot.com/2016/03/target-prediction-models-update.html) [code](https://github.com/madgpap/notebooks/blob/master/target_pred_21_demo.ipynb)]
* [ ] 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 targets and mechanisms of action, among others.
* [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. Drug (off-)targets.
* [ ] Human Metabolome Database [[paper]() [data](http://www.hmdb.ca/)]. Metabolizing enzymes.
* [ ] PIDGIN [[paper](https://dx.doi.org/10.1186%2Fs13321-015-0098-y) [code](https://github.com/lhm30/PIDGINv3)]. Target prediction trained with negative data.
* [ ] PubChem Bioassays [[paper](https://academic.oup.com/nar/article/45/D1/D955/2605812) [data](https://pubchem.ncbi.nlm.nih.gov/assay/bioactivity.cgi?tab=2)]. Repository of bioassay data.
* [ ] STITCH [[paper](https://dx.doi.org/10.1093%2Fnar%2Fgkv1277) [data](stitch.embl.de/)]. Integrative compound-protein interaction database. It has orthology mapping.
* [ ] Therapeutic Target Database [[paper](https://dx.doi.org/10.1093%2Fnar%2Fgkx1076) [data]( http://bidd.nus.edu.sg/group/ttd/ttd.asp)]. Mode of action of drugs.
* [ ] Vogt et al. Future Science OA (2018) [[paper](https://www.future-science.com/doi/10.4155/fsoa-2018-0050)]. Computationally derived compound profiling matrices.
* [ ] PIDGIN [[paper](https://dx.doi.org/10.1186%2Fs13321-015-0098-y) [code](https://github.com/lhm30/PIDGINv3)]. Target prediction trained with negative data.
* [X] ChEMBL drug target predictor [[blog](http://chembl.blogspot.com/2016/03/target-prediction-models-update.html) [code](https://github.com/madgpap/notebooks/blob/master/target_pred_21_demo.ipynb)]
### `C` Networks
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* [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.
* [ ] ChEMBL animal models [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6206617/)].
* [ ] 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.
......@@ -67,8 +66,7 @@ In addition, please be aware of the Bioteque project maintained by the SB&NB.
* [ ] PharmacoDB [[data](https://pharmacodb.pmgenomics.ca)]: Integrative pharmacogenomics resource across CCL panels.
* [X] DeepCodex [[data](http://deepcodex.org/) [paper](http://dx.doi.org/10.1021/acs.molpharmaceut.8b00284)]: An autoencoder of LINCS data.
* [ ] Paccmann [[data](https://github.com/drugilsberg/paccmann) [paper](https://arxiv.org/pdf/1904.11223.pdf)]: A cell sensitivity predictor based on chemical structure.
* [ ] Metabolomics profiling against E.coli. [[paper](https://www.sciencedirect.com/science/article/pii/S1097276519302710)]
* [ ] Animal models from ChEMBL [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6206617/)]
* [ ] Metabolomics profiling against E.coli [[paper](https://www.sciencedirect.com/science/article/pii/S1097276519302710)].
### `E` Clinics
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