The EMBL-EBI search and sequence analysis tools APIs in 2019
Open accessAbstract
The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The workflow runs on a regular basis, with resulting dataset indexed by EMBL-EBI search so it can be browsed and downloaded through BioModels web interface or programmatically.
“This workflow, depicted in Figure 1, runs on a regular basis, with the resulting dataset being indexed by the European Bioinformatics Institute (EMBL-EBI) search (Madeira et al., 2019; Park et al., 2017) so that it can be browsed and downloaded either through the BioModels web interface or programmatically.”
From BioModels Parameters: a treasure trove of parameter values from published systems biology models (2020) · cites this paper as Madeira et al., 2019
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works
Potter, S. C., Luciani, A., Eddy, S. R., Park, Y., Lopez, R., & Finn, R. D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky448 · Cited by 2,607 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 31
- [1]Tarkowska A., Carvalho-Silva D., Cook C.E., Turner E., Finn R.D., Yates A.D. Eleven quick tips to build a usable REST API for life sciences. PLoS Comput. Biol. 2018; 14: e1006542. 30543619 PMC6292566
- [2]Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L. BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10: 421. 20003500 PMC2803857
- [3]Pearson W.R., Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 1988; 85: 2444– 2448. 3162770 PMC280013
- [5]Jones P., Binns D., Chang H.Y., Fraser M., Li W., McAnulla C., McWilliam H., Maslen J., Mitchell A., Nuka G. et al. InterProScan 5: Genome-scale protein function classification. Bioinformatics. 2014; 30: 1236– 1240. 24451626 PMC3998142
- [6]Chojnacki S., Cowley A., Lee J., Foix A., Lopez R. Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. Nucleic Acids Res. 2017; 45: W550– W553. 28431173 PMC5570243
- [7]Park Y.M., Squizzato S., Buso N., Gur T., Lopez R. The EBI search engine: EBI search as a service - Making biological data accessible for all. Nucleic Acids Res. 2017; 45: W545– W549. 28472374 PMC5570174
- [8]Bateman A., Martin M.-J., Orchard S., Magrane M., Alpi E., Bely B., Bingley M., Britto R., Bursteinas B., Busiello G. et al. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2018; 47: D506– D515. PMC6323992 30395287
- [9]Silvester N., Alako B., Amid C., Cerdeño-Tarrága A., Clarke L., Cleland I., Harrison P.W., Jayathilaka S., Kay S., Keane T. et al. The European Nucleotide Archive in 2017. Nucleic Acids Res. 2018; 46: D36– D40. 29140475 PMC5753375
- [10]Kersey P.J., Allen J.E., Allot A., Barba M., Boddu S., Bolt B.J., Carvalho-Silva D., Christensen M., Davis P., Grabmueller C. et al. Ensembl Genomes 2018: An integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res. 2018; 46: D802– D808. 29092050 PMC5753204
- [11]Burley S.K., Berman H.M., Bhikadiya C., Bi C., Chen L., Costanzo L. Di, Christie C., Duarte J.M., Dutta S., Feng Z. et al. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res. 2018; 47: D520– D528. PMC6324056 30357364
- [12]Mitchell A.L., Attwood T.K., Babbitt P.C., Blum M., Bork P., Bridge A., Brown S.D., Chang H.-Y., El-Gebali S., Fraser M.I. et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2018; 47: D351– D360. PMC6323941 30398656
- [13]Dana J.M., Gutmanas A., Tyagi N., Qi G., O’Donovan C., Martin M., Velankar S. SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. Nucleic Acids Res. 2018; 47: 482– 489. PMC6324003 30445541
- [14]Sweeney B.A., Petrov A.I., Burkov B., Finn R.D., Bateman A., Szymanski M., Karlowski W.M., Gorodkin J., Seemann S.E., Cannone J.J. et al. RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res. 2018; 47: D221– D229. PMC6324050 30395267
- [15]Perez-Riverol Y., Bai M., da Veiga Leprevost F., Squizzato S., Park Y.M., Haug K., Carroll A.J., Spalding D., Paschall J., Wang M. et al. Discovering and linking public omics data sets using the Omics Discovery Index. Nat. Biotechnol. 2017; 35: 406– 409. 28486464 PMC5831141
- [17]Rice P., Longden L., Bleasby A. EMBOSS: The European molecular biology open software suite. Trends Genet. 2000; 16: 276– 277. 10827456
- [18]Waterhouse A.M., Procter J.B., Martin D.M.A., Clamp M., Barton G.J. Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009; 25: 1189– 1191. 19151095 PMC2672624
- [19]Ettwiller L., Paten B., Souren M., Loosli F., Wittbrodt J., Birney E. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol. 2005; 6: R104. 16356267 PMC1414082
- [20]Jareborg N., Birney E., Durbin R. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res. 1999; 9: 815– 824. 10508839 PMC310816
- [21]de Castro E., Sigrist C.J.A., Gattiker A., Bulliard V., Langendijk-Genevaux P.S., Gasteiger E., Bairoch A., Hulo N. ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 2006; 34: W362– W365. 16845026 PMC1538847
- [23]Berger S.A., Krompass D., Stamatakis A. Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst. Biol. 2011; 60: 291– 302. 21436105 PMC3078422
- [24]Rawlings N.D., Barrett A.J., Thomas P.D., Huang X., Bateman A., Finn R.D. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res. 2018; 46: D624– D632. 29145643 PMC5753285
- [25]Gaulton A., Hersey A., Nowotka M.L., Patricia Bento A., Chambers J., Mendez D., Mutowo P., Atkinson F., Bellis L.J., Cibrian-Uhalte E. et al. The ChEMBL database in 2017. Nucleic Acids Res. 2017; 45: D945– D954. 27899562 PMC5210557
- [26]Robinson J., Halliwell J.A., Hayhurst J.D., Flicek P., Parham P., Marsh S.G.E. The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Res. 2015; 43: D423– D431. 25414341 PMC4383959
- [27]Gou Y., Graff F., Kilian O., Kafkas S., Katuri J., Kim J.H., Marinos N., McEntyre J., Morrison A., Pi X. et al. Europe PMC: A full-text literature database for the life sciences and platform for innovation. Nucleic Acids Res. 2015; 43: D1042– D1048. 25378340 PMC4383902
- [28]Faulconbridge A., Burdett T., Brandizi M., Gostev M., Pereira R., Vasant D., Sarkans U., Brazma A., Parkinson H. Updates to BioSamples database at European Bioinformatics Institute. Nucleic Acids Res. 2014; 42: D50– D52. 24265224 PMC3965081
- [29]Kalvari I., Argasinska J., Quinones-Olvera N., Nawrocki E.P., Rivas E., Eddy S.R., Bateman A., Finn R.D., Petrov A.I. Rfam 13.0: Shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 2018; 46: D335– D342. 29112718 PMC5753348
- [30]Jupp S. et al. Malone J A new Ontology Lookup Service at EMBL-EBI. 2015; Proceedings of SWAT4LS International Conference 2015.
- [31]Tryka K.A., Hao L., Sturcke A., Jin Y., Wang Z.Y., Ziyabari L., Lee M., Popova N., Sharopova N., Kimura M. et al. NCBI’s database of genotypes and phenotypes: DbGaP. Nucleic Acids Res. 2014; 42: D975– D979. 24297256 PMC3965052
- [32]Cook C.E., Bergman M.T., Finn R.D., Cochrane G., Birney E., Apweiler R. The European Bioinformatics Institute in 2016: data growth and integration. Nucleic Acids Res. 2016; 44: D20– D26. 26673705 PMC4702932
- [33]Ison J., Rapacki K., Ménager H., Kalaš M., Rydza E., Chmura P., Anthon C., Beard N., Berka K., Bolser D. et al. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 2016; 44: D38– D47. 26538599 PMC4702812
- [34]McDowall M.D., Harris M.A., Lock A., Rutherford K., Staines D.M., Bähler J.Ü., Kersey P.J., Oliver S.G., Wood V. PomBase 2015: updates to the fission yeast database. Nucleic Acids Res. 2015; 43: D656– D661. 25361970 PMC4383888
Cited by
Sorted by citations
Hoffmann, M., Kleine-Weber, H., & Pöhlmann, S. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.022 · Cited by 1,852 · see citing works
Protein Sequence Analysis Using the MPI Bioinformatics Toolkit
Gabler, F., Nam, S., Till, S., Mirdita, M., Steinegger, M., Söding, J., Lupas, A. N., & Alva, V. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.108 · Cited by 831 · see citing works
Complete genomic and epigenetic maps of human centromeres
Altemose, N., Logsdon, G. A., Bzikadze, A. V., Sidhwani, P., Langley, S. A., Caldas, G. V., Hoyt, S. J., Uralsky, L., Ryabov, F. D., Shew, C. J., et al. (2022) · Science · doi:10.1126/science.abl4178 · Cited by 618 · see citing works
Sampling alternative conformational states of transporters and receptors with AlphaFold2
del Alamo, D., Sala, D., Mchaourab, H. S., & Meiler, J. (2022) · eLife · doi:10.7554/elife.75751 · Cited by 511 · see citing works
“…templates were used: OF MCT1 with FucB (PDB 3O7Pa and 3O7Qa, 18% sequence identity calculated using Needleman Wunsch Needleman and Wunsch, 1970 ; Madeira et al., 2019 ); OF LAT1 with AdiC (3OB6a and 5J4Ib, 22%); IF LAT1 with b(0,+)AT1 (6LI9, 45%), KCC3 (6Y5Ra, 12%), GkApcT (6F34a, 24%), NKCC1…”
Method<i>Enterococcus</i> peptidoglycan remodeling promotes checkpoint inhibitor cancer immunotherapy
Griffin, M. E., Espinosa, J., Becker, J. L., Luo, J.-D., Carroll, T. S., Jha, J. K., Fanger, G. R., & Hang, H. C. (2021) · Science · doi:10.1126/science.abc9113 · Cited by 366 · see citing works
Freyn, A. W., Ramos da Silva, J., Rosado, V. C., Bliss, C. M., Pine, M., Mui, B. L., Tam, Y. K., Madden, T. D., de Souza Ferreira, L. C., Weissman, D., et al. (2020) · Molecular Therapy · doi:10.1016/j.ymthe.2020.04.018 · Cited by 299 · see citing works
In-cell architecture of an actively transcribing-translating expressome
O’Reilly, F. J., Xue, L., Graziadei, A., Sinn, L., Lenz, S., Tegunov, D., Blötz, C., Singh, N., Hagen, W. J. H., Cramer, P., et al. (2020) · Science · doi:10.1126/science.abb3758 · Cited by 284 · see citing works
Martin, C. J., Datta, A., Littlefield, C., Kalra, A., Chapron, C., Wawersik, S., Dagbay, K. B., Brueckner, C. T., Nikiforov, A., Danehy, F. T., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aay8456 · Cited by 224 · see citing works
Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold
Fontana, P., Dong, Y., Pi, X., Tong, A. B., Hecksel, C. W., Wang, L., Fu, T.-M., Bustamante, C., & Wu, H. (2022) · Science · doi:10.1126/science.abm9326 · Cited by 195 · see citing works
Foley, M. H., Walker, M. E., Stewart, A. K., O’Flaherty, S., Gentry, E. C., Patel, S., Beaty, V. V., Allen, G., Pan, M., Simpson, J. B., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01337-7 · Cited by 181 · see citing works
Structure of Hsp90–p23–GR reveals the Hsp90 client-remodelling mechanism
Noddings, C. M., Wang, R. Y.-R., Johnson, J. L., & Agard, D. A. (2022) · Nature · doi:10.1038/s41586-021-04236-1 · Cited by 165 · see citing works
Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex
Gruszczyk, J., Grandvuillemin, L., Lai-Kee-Him, J., Paloni, M., Savva, C. G., Germain, P., Grimaldi, M., Boulahtouf, A., Kwong, H.-S., Bous, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34773-w · Cited by 137 · see citing works
Cross-species analysis of enhancer logic using deep learning
Minnoye, L., Taskiran, I. I., Mauduit, D., Fazio, M., Van Aerschot, L., Hulselmans, G., Christiaens, V., Makhzami, S., Seltenhammer, M., Karras, P., et al. (2020) · Genome Research · doi:10.1101/gr.260844.120 · Cited by 116 · see citing works
Santana, D. J., & O’Meara, T. R. (2021) · Nature Communications · doi:10.1038/s41467-021-27545-5 · Cited by 91 · see citing works
SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential
Vithani, N., Ward, M. D., Zimmerman, M. I., Novak, B., Borowsky, J. H., Singh, S., & Bowman, G. R. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.03.024 · Cited by 84 · see citing works
Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the glucocorticoid receptor
Noddings, C. M., Johnson, J. L., & Agard, D. A. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01128-y · Cited by 75 · see citing works
Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An emergent therapeutic target
Adams, O., Deme, J. C., Parker, J. L., Fowler, P. W., Lea, S. M., & Newstead, S. (2021) · Structure · doi:10.1016/j.str.2021.06.013 · Cited by 63 · see citing works
Mallack, E. J., Gao, K., Engelen, M., & Kemp, S. (2022) · Cells · doi:10.3390/cells11020283 · Cited by 60 · see citing works
A dynamic charge-charge interaction modulates PP2A:B56 substrate recruitment
Wang, X., Garvanska, D. H., Nasa, I., Ueki, Y., Zhang, G., Kettenbach, A. N., Peti, W., Nilsson, J., & Page, R. (2020) · eLife · doi:10.7554/elife.55966 · Cited by 53 · see citing works
Aiyer, S., Swapna, G. V. T., Ma, L.-C., Liu, G., Hao, J., Chalmers, G., Jacobs, B. C., Montelione, G. T., & Roth, M. J. (2021) · Structure · doi:10.1016/j.str.2021.01.010 · Cited by 35 · see citing works
Basavalingappa, R. H., Arumugam, R., Lasrado, N., Yalaka, B., Massilamany, C., Gangaplara, A., Riethoven, J.-J., Xiang, S.-H., Steffen, D., & Reddy, J. (2020) · Molecular Immunology · doi:10.1016/j.molimm.2020.06.017 · Cited by 29 · see citing works
Canestrari, J. G., Lasek‐Nesselquist, E., Upadhyay, A., Rofaeil, M., Champion, M. M., Wade, J. T., Derbyshire, K. M., & Gray, T. A. (2020) · Molecular Microbiology · doi:10.1111/mmi.14498 · Cited by 25 · see citing works
Wang, C., van Haperen, R., Gutiérrez-Álvarez, J., Li, W., Okba, N. M. A., Albulescu, I., Widjaja, I., van Dieren, B., Fernandez-Delgado, R., Sola, I., et al. (2020) · doi:10.1101/2020.10.20.346916 · Cited by 15 · see citing works
Fontenot, C. R., & Ding, H. (2022) · BioMetals · doi:10.1007/s10534-022-00390-9 · Cited by 17 · see citing works
Pedreira, T., Elfmann, C., Singh, N., & Stülke, J. (2022) · Protein Science · doi:10.1002/pro.4179 · Cited by 13 · see citing works
BioModels Parameters: a treasure trove of parameter values from published systems biology models
Glont, M., Arankalle, C., Tiwari, K., Nguyen, T. V. N., Hermjakob, H., & Malik-Sheriff, R. S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa560 · Cited by 10 · see citing works
Shugarts Devanapally, N. M., Sathya, A., Yi, A. L., Chan, W. M., Marre, J. A., & Jose, A. M. (2025) · eLife · doi:10.7554/elife.99149.3 · Cited by 6 · see citing works
- Authors
- Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., & Lopez, R.
- Affiliations
- European Bioinformatics Institute (GB)
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-04-12
- Volume
- 47
- Issue
- W1
- Pages
- W636-W641
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6602479
- OpenAlex
- W2938574745
- Cited by
- 4,167
- References
- 2
- Citations by year
- 2026: 69 · 2025: 135 · 2024: 280 · 2023: 438 · 2022: 976 · 2021: 1169 · 2020: 934 · 2019: 159 · 2012: 1
- FWCI
- 961.53
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- European Molecular Biology Laboratory (654039)
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- EMBL-EBI, bioinformatics web services, REST API, SOAP web services, sequence analysis tools, text search engines, data discoverability, biological data integration
- MeSH terms
- Software, Sequence Alignment, Sequence Analysis, Sequence Analysis, Protein, Databases, Nucleic Acid, Databases, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
