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BioSystics Analytics Platform™:
3rd Party Data & Software


External Data Sources

CHEMBL

ChEMBL Database: Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E, Davies M, Dedman N, Karlsson A, Magariños MP, Overington JP, Papadatos G, Smit I, Leach AR. (2017) 'The ChEMBL database in 2017.' Nucleic Acids Res., 45(D1) D945-D954.
PMC: PMC5210557 | DOI: 10.1093/nar/gkw1074

ChEMBL Web Services: Davies M, Nowotka M, Papadatos G, Dedman N, Gaulton A, Atkinson F, Bellis L, Overington JP. (2015) 'ChEMBL web services: streamlining access to drug discovery data and utilities.' Nucleic Acids Res., 43(W1) W612-W620.
PMC: PMC4489243 | DOI: 10.1093/nar/gkv352

ClinicalTrials.gov

Clustergrammer

Fernandez, N. F. et al. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. Sci. Data 4:170151 doi: 10.1038/sdata.2017.151 (2017).

European Medicines Agency

Enrichr

Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013; 128(14).

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377 .

Xie Z, Bailey A, Kuleshov MV, Clarke DJB., Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM, Jeon M, & Ma’ayan A. Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. 2021.
DOI: 10.1002/cpz1.90

Ensemble/BioMart

Fiona Cunningham , James E. Allen, Jamie Allen, Jorge Alvarez-Jarreta, M. Ridwan Amode, Irina M. Armean , Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis , Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins , Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron , Thiago Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier , Toby Hunt, Thomas Juettemann , Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, José Carlos Marugán, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N. Ogeh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Piliˇzota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, José G. Pérez-Silva, William Stark, Emily Steed, Kyösti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-G ́omez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Natalie Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish , Stefano Giorgetti, Leanne Haggerty, Sarah E. Hunt , Garth R. IIsley, Jane E. Loveland , Fergal J. Martin , Benjamin Moore, Jonathan M. Mudge, Matthieu Muffato, Emily Perry , Magali Ruffier , John Tate, David Thybert, Stephen J. Trevanion, Sarah Dyer, Peter W. Harrison , Kevin L. Howe , Andrew D. Yates , Daniel R. Zerbino and Paul Flicek Ensembl 2022. Nucleic Acids Res. 2022, vol. 50(1):D988-D995
PMID: 34791404 | DOI: 10.1093/nar/gkab1049

Harmonizome

Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016 Jul 3;2016. pii: baw100.

HUGO Gene Nomenclature Committee

Tweedie S, Braschi B, Gray KA, Jones TEM, Seal RL, Yates B, Bruford EA. Genenames.org: the HGNC and VGNC resources in 2021. Nucleic Acids Res.
PMID: 33152070 | PMCID: PMC7779007 | DOI: 10.1093/nar/gkaa980

LiverTox

NAMCS/NHAMCS

National Institute of Health's TempO-Seq Probes

OpenFDA

PubChem

Kim S, Chen J, Cheng T, et al. PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res. 2021;49(D1):D1388–D1395.
DOI: 10.1093/nar/gkaa971

PubMed

Rat Genome Database (RGD)

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. Smith JR, Hayman GT, Wang SJ, Laulederkind SJF, Hoffman MJ, Kaldunski ML, Tutaj M, Thota J, Nalabolu HS, Ellanki SLR, Tutaj MA, De Pons JL, Kwitek AE, Dwinell MR, Shimoyama ME. Nucleic Acids Res. 2019 Nov 12. pii: gkz1041.
PMID:31713623 | DOI: 10.1093/nar/gkz1041

ToxNet

Unichem

Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. (2013) UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5: 3 Chambers, J., Davies, M., Gaulton, A., Papadatos, G., Hersey and Overington, J.P. (2014) UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers. Journal of Cheminformatics 2014, 6: 43


3rd Software License Information

Click here to download a PDF detailing the licenses of third-party libraries distributed with the BioSystics-AP™.


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