ExPASy: SIB bioinformatics resource portal
Open accessAbstract
ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.
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?
Currently only 488 or 0.6% of over 80,000 known cell lines have been reported as misidentified, and most cell lines are used infrequently.
“(Although currently only 488 or 0.6% of over 80,000 known cell lines have been reported as misidentified, most cell lines are used infrequently [15].)”
From The ghosts of HeLa: How cell line misidentification contaminates the scientific literature (2017) · cites this paper as [15]
The paper’s ‘Access to a large set of bioinformatics resources’ and ‘Monitoring (availability and usage checks)’ sections discuss ExPASy resources, not cell lines. Searches for the 488/0.6% figure and for misidentified or infrequently used cell lines found no passage addressing either part of the claim. Page numbers were not available in our copy. (LLM, conf=0.78)
Experimental — accuracy not yet measuredAuthors are expected to check overviews of misidentified cells before conducting their experiments.
“In addition, authors are expected to check overviews of misidentified cells (such as [12, 15, 27, 31]) before conducting their experiments.”
From The ghosts of HeLa: How cell line misidentification contaminates the scientific literature (2017) · cites this paper as [15]
The Abstract and ‘Access to a large set of bioinformatics resources’ section describe ExPASy as a portal for databases and tools, not an overview of misidentified cells. Searches for misidentified or contaminated cell lines and pre-experiment checks found no passage addressing the claim. Page numbers are unavailable in our copy. (LLM, conf=0.76)
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: 3
- [1]Appel RD Bairoch A Hochstrasser DF A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server Trends Biochem. Sci. 1994 19 258 260 8073505
- [2]Gasteiger E Gattiker A Hoogland C Ivanyi I Appel RD Bairoch A ExPASy: The proteomics server for in-depth protein knowledge and analysis Nucleic Acids Res. 2003 31 3784 3788 12824418 PMC168970
- [3]Pettifer,S., Ison,J., Kalas,M., Thorne,D., McDermott,P., Jonassen,I., Liaquat,A., Fernández,J.M., Rodriguez,J.M., INB-Partners et al. (2010) The EMBRACE web service collection. Nucleic Acids Res., 38, W719–W723 PMC2896104 20462862
Cited by
Sorted by citations
The Cellosaurus, a Cell-Line Knowledge Resource
Bairoch, A. (2018) · Journal of Biomolecular Techniques JBT · doi:10.7171/jbt.18-2902-002 · Cited by 807 · see citing works
Lee, K. A., Thomas, A. M., Bolte, L. A., Björk, J. R., de Ruijter, L. K., Armanini, F., Asnicar, F., Blanco-Miguez, A., Board, R., Calbet-Llopart, N., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01695-5 · Cited by 464 · see citing works
Lahaye, X., Satoh, T., Gentili, M., Cerboni, S., Conrad, C., Hurbain, I., El Marjou, A., Lacabaratz, C., Lelièvre, J.-D., & Manel, N. (2013) · Immunity · doi:10.1016/j.immuni.2013.11.002 · Cited by 390 · see citing works
The ghosts of HeLa: How cell line misidentification contaminates the scientific literature
Horbach, S. P. J. M., & Halffman, W. (2017) · PLOS ONE · doi:10.1371/journal.pone.0186281 · Cited by 167 · see citing works
Microalgae with Artificial Intelligence: A Digitalized Perspective on Genetics, Systems and Products
Teng, S. Y., Yew, G. Y., Sukačová, K., Show, P. L., Máša, V., & Chang, J.-S. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107631 · Cited by 145 · see citing works
CLASTR: The Cellosaurus STR similarity search tool ‐ A precious help for cell line authentication
Robin, T., Capes‐Davis, A., & Bairoch, A. (2020) · International Journal of Cancer · doi:10.1002/ijc.32639 · Cited by 97 · see citing works
Mutation screening of SCN2A in schizophrenia and identification of a novel loss-of-function mutation
Carroll, L. S., Woolf, R., Ibrahim, Y., Williams, H. J., Dwyer, S., Walters, J., Kirov, G., O’Donovan, M. C., & Owen, M. J. (2016) · Psychiatric Genetics · doi:10.1097/ypg.0000000000000110 · Cited by 54 · see citing works
- Authors
- Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., de Castro, E., Duvaud, S., Flegel, V., Fortier, A., Gasteiger, E., Grosdidier, A., Hernandez, C., Ioannidis, V., Kuznetsov, D., Liechti, R., Moretti, S., Mostaguir, K., Redaschi, N., Rossier, G., Xenarios, I., & Stockinger, H.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-05-31
- Volume
- 40
- Issue
- W1
- Pages
- W597-W603
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3394269
- OpenAlex
- W2147533449
- Cited by
- 2,266
- References
- 0
- Citations by year
- 2026: 98 · 2025: 170 · 2024: 182 · 2023: 185 · 2022: 250 · 2021: 282 · 2020: 230 · 2019: 170 · 2018: 146 · 2017: 125 · 2016: 119 · 2015: 107 · 2014: 109 · 2013: 80 · 2012: 12
- FWCI
- 39.63
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- reroDoc Digital Library (submittedVersion)
- IRIS (submittedVersion, other-oa)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- HighWire Press Open Archive (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- proteomics database, web-based software tool, web interface design
- MeSH terms
- Computer Graphics, Software, User-Computer Interface, Systems Integration, Computational Biology, Internet, Genomics, Proteomics
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
