The EBI search engine: EBI search as a service—making biological data accessible for all
Open accessAbstract
We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include nucleotide and protein sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, as well as the life science literature. EBI Search provides a powerful RESTful API that enables its integration into third-party portals, thus providing 'Search as a Service' capabilities, which are the main topic of this article.
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 Park et al., 2017
The Data Coverage section lists BioModels among resources available through EBI Search and says the engine indexes data. The Abstract and Improved Search Findability and Usability section describe web retrieval and programmatic access. The paper does not identify this workflow or its resulting dataset, establish that it runs regularly, or say that this dataset can be browsed and downloaded through the BioModels interface. (LLM, conf=0.86)
Experimental — accuracy not yet measured
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
No references could be resolved yet.
Research works printed but not linked: 16
- [1]Squizzato S., Park Y.M., Buso N., Gur T., Cowley A., Li W., Uludag M., Pundir S., Cham J.A., McWilliam H. The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. Nucleic Acids Res. 2015; 43: W585– W588. 25855807 PMC4489232
- [2]Brooksbank C., Bergman M.T., Apweiler R., Birney E., Thornton J. The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res. 2014; 42: D18– D25. 24271396 PMC3964968
- [3]Alcántara R., Onwubiko J., Cao H., Matos Pd., Cham J.A., Jacobsen J., Holliday G.L., Fischer J.D., Rahman S.A., Jassal B. The EBI enzyme portal. Nucleic Acids Res. 41: d773– d780. 23175605 PMC3531056
- [4]Eric P Nawrocki., Sarah W Burge., Alex Bateman., Jennifer Daub, Ruth Y Eberhardt., Sean R Eddy., Evan W Floden., Paul P Gardner., Thomas A Jones., John Tate, Robert D Finn. Rfam 12.0: updates to the RNA families database. Nucleic Acids Research. Nucleic Acids Res. 2014; 43: D130– D137. 25392425 PMC4383904
- [5]Kersey P.J., Allen J.E., Armean I., Boddu S., Bolt B.J., Carvalho-Silva D., Christensen M., Davis P., Falin L.J., Grabmueller C. Ensembl Genomes: more genomes, more complexity. Nucleic Acids Res. 2016; 44: D574– D580. 26578574 PMC4702859
- [6]Ison J., Rapacki K., Ménager H., Kalaš M., Rydza E., Chmura P., Anthon C., Beard N., Berka K., Bolser D. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44: D38– D47. 26538599 PMC4702812
- [7]Mitchell A., Bucchini F., Cochrane G., Denise H., ten Hoopen P., Fraser M., Pesseat S., Potter S., Scheremetjew M., Sterk P. EBI metagenomics in 2016–an expanding and evolving resource for the analysis and archiving of metagenomic data. Nucleic Acids Res. 44: d595– d603. 26582919 PMC4702853
- [8]Finn R.D, Attwood T.K, Babbitt P.C, Bateman A., Bork P., Bridge A.J, Chang H.Y., Dosztányi Z., El-Gebali S., Fraser M. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 45: D190– D199. 27899635 PMC5210578
- [9]Toribio A.L., Alako B., Amid C., Cerdeño-Tarrága A., Clarke L., Cleland I., Fairley S., Gibson R., Goodgame N., Ten Hoopen P. European Nucleotide Archive in 2016. Nucleic Acids Res. 2016; 45: D32– D36. 27899630 PMC5210577
- [10]Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L. BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10: 421– 430. 20003500 PMC2803857
- [11]Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Söding J. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011; 7: 539– 544. 21988835 PMC3261699
- [12]Leinonen R., Nardone F., Zhu W., Apweiler R UniSave: the UniProtKB Sequence/Annotation Version database. Bioinformatics. 2006; 22: 1284– 1285. 16551660
- [13]Li W., Cowley A., Uludag M., Gur T., McWilliam H., Squizzato S., Park Y.M., Buso N., Lopez R. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res. 43: w580– w584. 25845596 PMC4489272
- [14]The UniProt Consortium UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45: D158– D169. 27899622 PMC5210571
- [15]Federhen S. The NCBI Taxonomy database. Nucleic Acids Res. 2011; 40: D136– D143. 22139910 PMC3245000
- [16]Gaulton A., Hersey A., Nowotka M., Bento A.P., Chambers J., Mendez D., Mutowo P., Atkinson F., Bellis L.J., Cibrián-Uhalte E. The ChEMBL database in 2017. Nucleic Acids Res. 2017; 45: D945– D954. 27899562 PMC5210557
Cited by
Sorted by citations
The Pfam protein families database in 2019
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky995 · Cited by 4,602 · 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-citationA harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
Variant Interpretation for Cancer Consortium, Wagner, A. H., Walsh, B., Mayfield, G., Tamborero, D., Sonkin, D., Krysiak, K., Deu-Pons, J., Duren, R. P., Gao, J., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0603-8 · Cited by 164 · see citing works
BioModels: expanding horizons to include more modelling approaches and formats
Glont, M., Nguyen, T. V. N., Graesslin, M., Hälke, R., Ali, R., Schramm, J., Wimalaratne, S. M., Kothamachu, V. B., Rodriguez, N., Swat, M. J., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1023 · Cited by 89 · 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
- Authors
- Park, Y. M., Squizzato, S., Buso, N., Gur, T., & Lopez, R.
- Affiliations
- European Bioinformatics Institute (GB)
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-05-02
- Volume
- 45
- Issue
- W1
- Pages
- W545-W549
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5570174
- OpenAlex
- W2610786720
- Cited by
- 33
- References
- 0
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 1 · 2021: 3 · 2020: 6 · 2019: 12 · 2018: 7 · 2017: 2
- FWCI
- 11.89
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- European Bioinformatics Institute
- European Molecular Biology Laboratory
- European Commission (676559)
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM094231)
- 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 › Bioinformatics and Genomic Networks
- Keywords
- REST API, data navigation, sequence data, protein families, macromolecular structure, data integration
- MeSH terms
- Enzymes, Genes, Proteins, Sequence Analysis, Internet, Search Engine
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
