The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
Accomplishments and challenges in literature data mining for biology
Open accessAbstract
We review recent results in literature data mining for biology and discuss the need and the steps for a challenge evaluation for this field. Literature data mining has progressed from simple recognition of terms to extraction of interaction relationships from complex sentences, and has broadened from recognition of protein interactions to a range of problems such as improving homology search, identifying cellular location, and so on. To encourage participation and accelerate progress in this expanding field, we propose creating challenge evaluations, and we describe two specific applications in this context. Contact: wuc@georgetown.edutsujii@is.s.u-tokyo.ac.jppark@nlp.kaist.ac.krlynette@mitre.orglimsoon@lit.org.sg * To whom correspondence should be addressed.
Overview
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
Verification
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.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Measuring the Accuracy of Diagnostic Systems
Swets, J. A. (1988) · Science · doi:10.1126/science.3287615 · Cited by 10,058
The SWISS-PROT protein sequence data bank and its supplement TrEMBL
Bairoch, A., & Apweiler, R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.31 · Cited by 3,587
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998
Bairoch, A. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.38 · Cited by 3,280
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
Bairoch, A. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.45 · Cited by 3,093
Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., et al. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902003451 · Cited by 2,577
Xenarios, I. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.303 · Cited by 1,741
BIND--The Biomolecular Interaction Network Database
Bader, G. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.242 · Cited by 1,560
BIND: the Biomolecular Interaction Network Database
Bader, G. D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg056 · Cited by 1,114
Creating the Gene Ontology Resource: Design and Implementation
Consortium, T. G. O. (2001) · Genome Research · doi:10.1101/gr.180801 · Cited by 956
RefSeq and LocusLink: NCBI gene-centered resources
Pruitt, K. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.137 · Cited by 893
Cited by
The text mining handbook: advanced approaches in analyzing unstructured data
(2007) · Choice Reviews Online · doi:10.5860/choice.44-5684 · Cited by 1,598
Literature mining for the biologist: from information retrieval to biological discovery
Jensen, L. J., Saric, J., & Bork, P. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1768 · Cited by 631
BioInfer: a corpus for information extraction in the biomedical domain
Pyysalo, S., Ginter, F., Heimonen, J., Björne, J., Boberg, J., Järvinen, J., & Salakoski, T. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-50 · Cited by 485
Text mining and its potential applications in systems biology
Ananiadou, S., Kell, D. B., & Tsujii, J.-I. (2006) · Trends in Biotechnology · doi:10.1016/j.tibtech.2006.10.002 · Cited by 324
Self-citationLearning about the world through long-term query logs
Richardson, M. (2008) · ACM Transactions on the Web · doi:10.1145/1409220.1409224 · Cited by 77
Metadata
- Authors
- Hirschman, L., Park, J. C., Tsujii, J., Wong, L., & Wu, C. H.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-12-01
- Volume
- 18
- Issue
- 12
- Pages
- 1553-1561
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2152183901
- Cited by
- 287
- References
- 43
- FWCI
- 11.77
- Type
- journal article
- Language
- en
- Open access
- bronze
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Accomplishments and challenges in literature data mining for biology. https://app.cochat.ai/papers/10.1093/bioinformatics/18.12.1553
- The paper
- Hirschman, L., Park, J. C., Tsujii, J., Wong, L., & Wu, C. H. (2002). Accomplishments and challenges in literature data mining for biology. Bioinformatics. https://doi.org/10.1093/bioinformatics/18.12.1553
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
