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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, 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 data releases. Also, the [LINCS Data Portal](http://lincsportal.ccs.miami.edu) is of 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.
In addition, please be aware of the Bioteque project maintained by the SB&NB. In addition, please be aware of the Bioteque project maintained by the SB&NB.
...@@ -13,148 +13,78 @@ In addition, please be aware of the Bioteque project maintained by the SB&NB. ...@@ -13,148 +13,78 @@ In addition, please be aware of the Bioteque project maintained by the SB&NB.
### `A` Chemistry ### `A` Chemistry
* [ ] ChemoPy [[paper](https://academic.oup.com/bioinformatics/article/29/8/1092/233093) [code]( http://code.google.com/p/pychem/downloads/list)] * [ ] ChemoPy [[paper](https://academic.oup.com/bioinformatics/article/29/8/1092/233093) [code]( http://code.google.com/p/pychem/downloads/list)]: A small chemoinformatics library focused on physicochemical properties and some fingerprints.
* A small chemoinformatics library focused on physicochemical properties and some fingerprints. * [ ] ClassyFire [[paper](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-016-0174-y) [code](https://bitbucket.org/wishartlab/classyfire_api)]: Automatic classification of chemical compounds. Ontology / taxonomy
* [ ] ClassyFire [[paper](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-016-0174-y) [code](https://bitbucket.org/wishartlab/classyfire_api)] * [ ] DeepChem [[web](http://deepchem.io) [code](https://deepchem.io/docs/deepchem.html)]: A powerful deep learning chemoinformatics library, containing a large number of featurizers. The RDKitDescriptors featurizer is also interesting.
* Automatic classification of chemical compounds * [X] E3FP [[paper](https://pubs.acs.org/doi/10.1021/acs.jmedchem.7b00696) [code](https://github.com/keiserlab/e3fp)]: Hashed representations of 3D molecular structure.
* Ontology / taxonomy * [ ] molBLOCKS [[paper](https://academic.oup.com/bioinformatics/article/30/14/2081/2391178) [code](http://compbio.cs.princeton.edu/molblocks)]. Decompose small molecules into fragments (scaffolds).
* [ ] DeepChem [[web](http://deepchem.io) [code](https://deepchem.io/docs/deepchem.html)] * [ ] PyBioMed [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861255/) [code]( http://projects.scbdd.com/pybiomed.html)]. A number of physicochemical descriptors and the common fingerprints. Very similar to ChemoPy. It can also featurize sequence data (protein and DNA).
* A powerful deep learning chemoinformatics library, containing a large number of featurizers. * [X] RDKIT [[paper]() [code](https://www.rdkit.org/)]. The standard library for chemoinformatics in `python`. It calculates several fingerprints and also does 3D conformational sampling.
* Among the interesting featurizers, there are the PDB-crystal embeddings, which should, in principle, enable connectivity between crystals and small molecules. * [X] Silicos-IT [[web](http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/) [code](http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/biscu-it/biscu-it.html)]. It has implementations for the [chemical beauty](https://www.ncbi.nlm.nih.gov/pubmed/22270643) score (QED).
* The RDKitDescriptors featurizer is also quite interesting. * [ ] Synthetic accessibility score [[code](https://github.com/mkusner/grammarVAE/blob/master/molecule_optimization/latent_features_and_targets_character/sascorer.py)]. A simple synthetic accessibility score.
* [X] E3FP [[paper](https://pubs.acs.org/doi/10.1021/acs.jmedchem.7b00696) [code](https://github.com/keiserlab/e3fp)]
* Simple representations of 3D molecular structure.
* Integrated tightly with RDKIT.
* [ ] molBLOCKS [[paper](https://academic.oup.com/bioinformatics/article/30/14/2081/2391178) [code](http://compbio.cs.princeton.edu/molblocks)]
* Decompose small molecules into fragments (scaffolds).
* [ ] PyBioMed [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861255/) [code]( http://projects.scbdd.com/pybiomed.html)]
* A number of physicochemical descriptors and the common fingerprints. Very similar to ChemoPy.
* It can also featurize sequence data (protein and DNA).
* [X] RDKIT [[paper]() [code](https://www.rdkit.org/)]
* The standard library for chemoinformatics in `python`.
* Calculates several fingerprints and also does 3D conformational sampling.
* [X] Silicos-IT [[web](http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/) [code](http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/biscu-it/biscu-it.html)]
* It has implementations for the [chemical beauty](https://www.ncbi.nlm.nih.gov/pubmed/22270643) score (QED).
* [ ] Synthetic accessibility score [[code](https://github.com/mkusner/grammarVAE/blob/master/molecule_optimization/latent_features_and_targets_character/sascorer.py)]
### `B` Targets ### `B` Targets
* [X] BindingDB [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702793/) [data](https://www.bindingdb.org/)] * [X] BindingDB [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702793/) [data](https://www.bindingdb.org/)]. Chemical-protein binding data (patents).
* 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 [[paper](https://academic.oup.com/nar/article/45/D1/D945/2605707) [data](https://www.ebi.ac.uk/chembl/)] * [ ] 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.
* Known drug targets * [ ] 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.
* Drug metabolizing enzymes * [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.
* Chemical-protein binding * [ ] Human Metabolome Database [[paper]() [data](http://www.hmdb.ca/)]. Metabolizing enzymes.
* Chemical-target-based assay activity * [ ] 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.
* [ ] Comparative Toxicogenomics Database (CTD) [[paper](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky868/5106145) [data](http://ctdbase.org/)] * [ ] STITCH [[paper](https://dx.doi.org/10.1093%2Fnar%2Fgkv1277) [data](stitch.embl.de/)]. Integrative compound-protein interaction database. It has orthology mapping.
* Chemical-gene interaction data, including regulatory interactions * [ ] 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.
* [ ] 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)] * [ ] Vogt et al. Future Science OA (2018) [[paper](https://www.future-science.com/doi/10.4155/fsoa-2018-0050)]. Computationally derived compound profiling matrices.
* Drug indications * [ ] 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] DrugBank [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753335/) [data](https://www.drugbank.ca/)] * [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)]
* Known drug targets with pharmacological action
* Drug metabolizing enzymes
* Drug (off-)targets
* [ ] Human Metabolome Database [[paper]() [data](http://www.hmdb.ca/)]
* Metabolizing enzymes
* [ ] LINCS touchstone targets [[paper](https://www.cell.com/cell/fulltext/S0092-8674(17)31309-0) [data](https://clue.io/touchstone)]
* Well annotated targets of a reference set of molecules
* [ ] 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
* It contains softly-annotated targets
* [ScrubChem](http://www.scrubchem.org/Home) is a digital curation of PubChem Bioassay (694 million bioactivities, 9,000 molecular targets, 2.3 million chemicals)
* [ ] 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
### `C` Networks ### `C` Networks
* [X] Chemical Entities of Biological Interest (ChEBI) [[paper](https://academic.oup.com/nar/article/44/D1/D1214/2502583) [data](https://www.ebi.ac.uk/chebi/)] * [X] Chemical Entities of Biological Interest (ChEBI) [[paper](https://academic.oup.com/nar/article/44/D1/D1214/2502583) [data](https://www.ebi.ac.uk/chebi/)]. Chemical ontology of biological roles.
* 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] InWEB [[paper](https://dx.doi.org/10.1038%2Fnmeth.4083) [data](https://www.intomics.com/inbio/map.html)] * [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.
* Integrative protein interaction database * [X] MetaPhORS [[paper](https://academic.oup.com/nar/article/39/5/e32/2409505) [data](orthology.phylomedb.org/)]. Orthology and paralogy relationships between genes.
* [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/)] * [X] PathwayCommons [[paper](https://academic.oup.com/nar/article/39/suppl_1/D685/2506078) [data](https://www.pathwaycommons.org/)]. Integrative interaction database, using pathway data.
* A standard pathway database * [X] Reactome [[paper](https://dx.doi.org/10.1093%2Fnar%2Fgkv1351) [data](https://reactome.org/)]. A standard pathway database.
* [X] MetaPhORS [[paper](https://academic.oup.com/nar/article/39/5/e32/2409505) [data](orthology.phylomedb.org/)] * [X] Recon [[paper](https://www.nature.com/articles/nbt.2488) [data](https://www.vmh.life/#home)]. Currently, we are using version 1 of Recon.
* Orthology and paralogy relationships between genes * [X] STRING [[paper](https://dx.doi.org/10.1093%2Fnar%2Fgkw937) [data](https://string-db.org/)]. Protein interaction database. Includes physical and regulatory interactions.
* [X] PathwayCommons [[paper](https://academic.oup.com/nar/article/39/suppl_1/D685/2506078) [data](https://www.pathwaycommons.org/)] * [ ] DoroThea [[resource](http://dorothea.opentargets.io/#/investigation/1)]. TF-drug interactions (only about 200 drugs).
* Integrative interaction database, using pathway data * [ ] Small Molecule Pathway Database [[paper](https://www.ncbi.nlm.nih.gov/pubmed/24203708) [data](http://smpdb.ca/)]. Well annotated small molecule pathways.
* [X] Reactome [[paper](https://dx.doi.org/10.1093%2Fnar%2Fgkv1351) [data](https://reactome.org/)]
* A standard pathway database
* [X] Recon [[paper](https://www.nature.com/articles/nbt.2488) [data](https://www.vmh.life/#home)]
* Currently, we are using version 1 of Recon.
* [X] STRING [[paper](https://dx.doi.org/10.1093%2Fnar%2Fgkw937) [data](https://string-db.org/)]
* Protein interaction database
* Includes physical and regulatory interactions
* [ ] DoroThea [[resource](http://dorothea.opentargets.io/#/investigation/1)]
* Transcription factor - drug interactions (only 200+).
### `D` Cells ### `D` Cells
* [X] Broad Therapeutics morphology data [[paper](www.pnas.org/content/111/30/10911) [data](http://lincsportal.ccs.miami.edu/datasets/view/LDS-1195)] * [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.
* 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.
* [ ] 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)] * [X] ChEMBL [[paper](https://academic.oup.com/nar/article/45/D1/D945/2605707) [data](https://www.ebi.ac.uk/chembl/)]. Literature cell-based assays.
* Large cell line panel of drug sensitivity profiles. * [ ] Clue.io morphology [[data](https://clue.io/morphology)]. Cell painting assay.
* [X] ChEMBL [[paper](https://academic.oup.com/nar/article/45/D1/D945/2605707) [data](https://www.ebi.ac.uk/chembl/)] * [ ] 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.
* Literature cell-based assays * [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.
* [ ] Clue.io morphology [[data](https://clue.io/morphology)] * [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.
* Cell painting assay * [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.
* [ ] Genomics of Cell Sensitivity in Cancer (GDSC) [[paper](https://www.cell.com/fulltext/S0092-8674(16)30746-2) [data](https://www.cancerrxgene.org/)] * [ ] DepMap [[data](https://depmap.org/portal/download/)]. Genetic screens in cancer.
* 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
* [ ] DepMap [[data](https://depmap.org/portal/download/)]
* Genetic screens in cancer.
* [ ] Non-antibiotic drugs on microbiome [[paper](https://www.nature.com/articles/nature25979)] * [ ] Non-antibiotic drugs on microbiome [[paper](https://www.nature.com/articles/nature25979)]
* Also, possibly, drug combinations [[data](https://www.nature.com/articles/s41586-018-0278-9?_ga=2.175924836.75233071.1541289600-2021366473.1541289600)] * [ ] Anti-biotic drug combinations [[data](https://www.nature.com/articles/s41586-018-0278-9?_ga=2.175924836.75233071.1541289600-2021366473.1541289600)]
* [ ] Consensus signatures from LINCS L1000 [[data](https://figshare.com/articles/Consensus_signatures_for_LINCS_L1000_perturbations/)] * [ ] Consensus LINCS L1000 signatures from ThinkLab [[data](https://figshare.com/articles/Consensus_signatures_for_LINCS_L1000_perturbations/)].
* [ ] 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.
### `E` Clinics ### `E` Clinics
* [ ] ADReCS [[data](http://bioinf.xmu.edu.cn/ADReCS/index.jsp)] * [ ] ADReCS [[data](http://bioinf.xmu.edu.cn/ADReCS/index.jsp)]. Side effects data.
* Side effects data. * [ ] AEOLUS [[paper](https://www.nature.com/articles/sdata201626) [data](http://mychem.info/)]. Side effect data.
* [ ] AEOLUS [[paper](https://www.nature.com/articles/sdata201626) [data](http://mychem.info/)] * [X] ChEMBL [[paper](https://academic.oup.com/nar/article/45/D1/D945/2605707) [data](https://www.ebi.ac.uk/chembl/)]. Drug indications. Therapeutic areas.
* Side effect data. * [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
* [X] ChEMBL [[paper](https://academic.oup.com/nar/article/45/D1/D945/2605707) [data](https://www.ebi.ac.uk/chembl/)] * [ ] 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 and therapeutic areas.
* Drug indications * [X] DrugBank [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753335/) [data](https://www.drugbank.ca/)]. Drug-drug interactions. Therapeutic areas.
* 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] Comparative Toxicogenomics Database (CTD) [[paper](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky868/5106145) [data](http://ctdbase.org/)] * [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.
* Compound-disease associations * [ ] Ginas [[data](https://tripod.nih.gov/ginas/)]. Software for registering substances.
* [ ] 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)] * [ ] OFFSIDES [[paper](http://stm.sciencemag.org/content/4/125/125ra31.long) [data](https://www.pharmgkb.org/downloads)]. Side effects extracted from hospital medical records.
* Drug indications * [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] DrugBank [[paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753335/) [data](https://www.drugbank.ca/)] * [X] RepoDB [[paper](https://www.nature.com/articles/sdata201729) [data](apps.chiragjpgroup.org/repoDB/)]. Drug indications.
* Drug-drug interactions * [ ] TWOSIDES [[paper](http://stm.sciencemag.org/content/4/125/125ra31.long) [data](https://www.pharmgkb.org/downloads)]. Drug-drug interactions.
* Therapeutic areas * [ ] Wikipedia [[paper](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-015-0061-y) [data](http://www.cheminfo.org/wikipedia/#)]. Wikipedia pages.
* [ ] DrugCentral [[paper](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky963/5146206) [data](http://drugcentral.org)] * [ ] Tox21 [[data]()]. A panel of 12 NR/SR pathways related to toxicity.
* Drug indications * [ ] ToxCast [[data]()]. A panel of >600 features related to toxicity.
* Drug side effects * [ ] eToxLab [[paper](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-015-0058-6) [data](https://github.com/phi-grib/eTOXlab)]: A framework for predictive toxicology.
* [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 \ No newline at end of file
* [ ] Ginas [[data](https://tripod.nih.gov/ginas/)]
* [ ] 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
* [ ] Wikipedia [[paper](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-015-0061-y) [data](http://www.cheminfo.org/wikipedia/#)]
* Wikipedia pages
## Prediction and calculation methods
:warning: This section is largely incomplete because we haven't explored it properly, yet.
* [ ] PIDGIN [[paper](https://dx.doi.org/10.1186%2Fs13321-015-0098-y) [code](https://github.com/lhm30/PIDGINv3)]
* Target prediction trained with negative data.
* [ ] 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)]
* [ ] eTOXlab [paper](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-015-0058-6)