DOI: 10.1016/s0378-1119(00)00431-5. Using BLAST for identifying gene and protein names in journal articles

Using BLAST for identifying gene and protein names in journal articles

10.1016/s0378-1119(00)00431-5

Crossref journal-article

Elsevier BV

Gene (78)

Bibliography

Krauthammer, M., Rzhetsky, A., Morozov, P., & Friedman, C. (2000). Using BLAST for identifying gene and protein names in journal articles. Gene, 259(1â2), 245â252.

Authors 4

Michael Krauthammer (first)
Andrey Rzhetsky (additional)
Pavel Morozov (additional)
Carol Friedman (additional)

References 16 Referenced 119

10.1016/S0022-2836(05)80360-2 / J. Mol. Biol. / Basic local alignment search tool by Altschul (1990)
10.1093/nar/25.17.3389 / Nucleic Acids Res. / Gapped BLAST and PSI-BLAST: a new generation of protein database search programs by Altschul (1997)
10.1093/nar/26.1.1 / Nucleic Acids Res. / GenBank by Benson (1998)
{'key': '10.1016/S0378-1119(00)00431-5_REF4', 'series-title': 'Perl Cookbook', 'author': 'Christiansen', 'year': '1998'} / Perl Cookbook by Christiansen (1998)
{'key': '10.1016/S0378-1119(00)00431-5_REF5', 'series-title': 'Proceedings of the National Academy of Science of the USA', 'first-page': '416', 'article-title': 'Codes without commas', 'author': 'Crick', 'year': '1957'} / Proceedings of the National Academy of Science of the USA / Codes without commas by Crick (1957)
{'key': '10.1016/S0378-1119(00)00431-5_REF6', 'first-page': '595', 'article-title': 'Towards a comprehensive medical language processing system: methods and issues', 'author': 'Friedman', 'year': '1997', 'journal-title': 'Proc. AMIA Ann. Fall Symp.'} / Proc. AMIA Ann. Fall Symp. / Towards a comprehensive medical language processing system: methods and issues by Friedman (1997)
{'key': '10.1016/S0378-1119(00)00431-5_REF7', 'first-page': '707', 'article-title': 'Toward information extraction: identifying protein names from biological papers', 'author': 'Fukuda', 'year': '1998', 'journal-title': 'Pac. Symp. Biocomput.'} / Pac. Symp. Biocomput. / Toward information extraction: identifying protein names from biological papers by Fukuda (1998)
{'key': '10.1016/S0378-1119(00)00431-5_REF8', 'series-title': 'Algorithms on strings, trees and sequences: computer science and computational biology', 'author': 'Gusfield', 'year': '1997'} / Algorithms on strings, trees and sequences: computer science and computational biology by Gusfield (1997)
10.7326/0003-4819-122-9-199505010-00007 / Ann. Intern. Med. / Unlocking clinical data from narrative reports: a study of natural language processing (see comments) by Hripcsak (1995)
10.1016/S0378-1119(00)00458-3 / Gene / A graphic editor for analyzing signal transduction pathways by Koike (2000)
{'key': '10.1016/S0378-1119(00)00431-5_REF11', 'series-title': 'Molecular Evolutionary Genetics', 'author': 'Nei', 'year': '1987'} / Molecular Evolutionary Genetics by Nei (1987)
{'key': '10.1016/S0378-1119(00)00431-5_REF12', 'first-page': '127', 'article-title': 'Mining molecular binding terminology from biomedical text', 'author': 'Rindflesch', 'year': '1999', 'journal-title': 'Proc. AMIA Symp.'} / Proc. AMIA Symp. / Mining molecular binding terminology from biomedical text by Rindflesch (1999)
10.1093/bioinformatics/16.12.1120 / Bioinformatics / A knowledge model for analysis and simulation of regulatory networks by Rzhetsky (2000)
10.1016/S1046-2023(05)80165-3 / Methods Enzymol. / Improved sensitivity of nucleic acid database searches using application-specific scoring matrices by States (1991)
{'key': '10.1016/S0378-1119(00)00431-5_REF15', 'series-title': 'Proceedings of the Fifth Message Understanding Conference (MUC-5)', 'first-page': '53', 'article-title': 'Comparing human and machine performance for natural language information evaluation', 'author': 'Will', 'year': '1994'} / Proceedings of the Fifth Message Understanding Conference (MUC-5) / Comparing human and machine performance for natural language information evaluation by Will (1994)
10.1016/S0033-8389(22)01511-1 / Radiol. Clin. North Am. / The statistical assessment of the variability in observer perception and description of roentgenographic pulmonary shadows by Yerushalmy (1969)

Dates

Type	When
Created	23 years, 1 month ago (July 25, 2002, 1:19 p.m.)
Deposited	2 years, 4 months ago (April 10, 2023, 6:43 p.m.)
Indexed	2 months, 1 week ago (June 17, 2025, 4:46 a.m.)
Issued	24 years, 8 months ago (Dec. 1, 2000)
Published	24 years, 8 months ago (Dec. 1, 2000)
Published Print	24 years, 8 months ago (Dec. 1, 2000)

Funders 0

None

BibTeX

@article{Krauthammer_2000, title={Using BLAST for identifying gene and protein names in journal articles}, volume={259}, ISSN={0378-1119}, url={http://dx.doi.org/10.1016/s0378-1119(00)00431-5}, DOI={10.1016/s0378-1119(00)00431-5}, number={1–2}, journal={Gene}, publisher={Elsevier BV}, author={Krauthammer, Michael and Rzhetsky, Andrey and Morozov, Pavel and Friedman, Carol}, year={2000}, month=dec, pages={245–252} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        6,
        17
      ]
    ],
    "date-time": "2025-06-17T08:46:14Z",
    "timestamp": 1750149974367
  },
  "reference-count": 16,
  "publisher": "Elsevier BV",
  "issue": "1-2",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2000,
            12,
            1
          ]
        ],
        "date-time": "2000-12-01T00:00:00Z",
        "timestamp": 975628800000
      },
      "content-version": "tdm",
      "delay-in-days": 0,
      "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2000,
        12
      ]
    ]
  },
  "DOI": "10.1016/s0378-1119(00)00431-5",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2002,
        7,
        25
      ]
    ],
    "date-time": "2002-07-25T17:19:02Z",
    "timestamp": 1027617542000
  },
  "page": "245-252",
  "source": "Crossref",
  "is-referenced-by-count": 119,
  "title": "Using BLAST for identifying gene and protein names in journal articles",
  "prefix": "10.1016",
  "volume": "259",
  "author": [
    {
      "given": "Michael",
      "family": "Krauthammer",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Andrey",
      "family": "Rzhetsky",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Pavel",
      "family": "Morozov",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Carol",
      "family": "Friedman",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "78",
  "reference": [
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF1",
      "doi-asserted-by": "crossref",
      "first-page": "403",
      "DOI": "10.1016/S0022-2836(05)80360-2",
      "article-title": "Basic local alignment search tool",
      "volume": "215",
      "author": "Altschul",
      "year": "1990",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF2",
      "doi-asserted-by": "crossref",
      "first-page": "3389",
      "DOI": "10.1093/nar/25.17.3389",
      "article-title": "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs",
      "volume": "25",
      "author": "Altschul",
      "year": "1997",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF3",
      "doi-asserted-by": "crossref",
      "first-page": "1",
      "DOI": "10.1093/nar/26.1.1",
      "article-title": "GenBank",
      "volume": "26",
      "author": "Benson",
      "year": "1998",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF4",
      "series-title": "Perl Cookbook",
      "author": "Christiansen",
      "year": "1998"
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF5",
      "series-title": "Proceedings of the National Academy of Science of the USA",
      "first-page": "416",
      "article-title": "Codes without commas",
      "author": "Crick",
      "year": "1957"
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF6",
      "first-page": "595",
      "article-title": "Towards a comprehensive medical language processing system: methods and issues",
      "author": "Friedman",
      "year": "1997",
      "journal-title": "Proc. AMIA Ann. Fall Symp."
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF7",
      "first-page": "707",
      "article-title": "Toward information extraction: identifying protein names from biological papers",
      "author": "Fukuda",
      "year": "1998",
      "journal-title": "Pac. Symp. Biocomput."
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF8",
      "series-title": "Algorithms on strings, trees and sequences: computer science and computational biology",
      "author": "Gusfield",
      "year": "1997"
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF9",
      "doi-asserted-by": "crossref",
      "first-page": "681",
      "DOI": "10.7326/0003-4819-122-9-199505010-00007",
      "article-title": "Unlocking clinical data from narrative reports: a study of natural language processing (see comments)",
      "volume": "122",
      "author": "Hripcsak",
      "year": "1995",
      "journal-title": "Ann. Intern. Med."
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF10",
      "doi-asserted-by": "crossref",
      "DOI": "10.1016/S0378-1119(00)00458-3",
      "article-title": "A graphic editor for analyzing signal transduction pathways",
      "author": "Koike",
      "year": "2000",
      "journal-title": "Gene"
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF11",
      "series-title": "Molecular Evolutionary Genetics",
      "author": "Nei",
      "year": "1987"
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF12",
      "first-page": "127",
      "article-title": "Mining molecular binding terminology from biomedical text",
      "author": "Rindflesch",
      "year": "1999",
      "journal-title": "Proc. AMIA Symp."
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF13",
      "doi-asserted-by": "crossref",
      "DOI": "10.1093/bioinformatics/16.12.1120",
      "article-title": "A knowledge model for analysis and simulation of regulatory networks",
      "author": "Rzhetsky",
      "year": "2000",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF14",
      "doi-asserted-by": "crossref",
      "first-page": "66",
      "DOI": "10.1016/S1046-2023(05)80165-3",
      "article-title": "Improved sensitivity of nucleic acid database searches using application-specific scoring matrices",
      "volume": "3",
      "author": "States",
      "year": "1991",
      "journal-title": "Methods Enzymol."
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF15",
      "series-title": "Proceedings of the Fifth Message Understanding Conference (MUC-5)",
      "first-page": "53",
      "article-title": "Comparing human and machine performance for natural language information evaluation",
      "author": "Will",
      "year": "1994"
    },
    {
      "key": "10.1016/S0378-1119(00)00431-5_REF16",
      "doi-asserted-by": "crossref",
      "first-page": "381",
      "DOI": "10.1016/S0033-8389(22)01511-1",
      "article-title": "The statistical assessment of the variability in observer perception and description of roentgenographic pulmonary shadows",
      "volume": "7",
      "author": "Yerushalmy",
      "year": "1969",
      "journal-title": "Radiol. Clin. North Am."
    }
  ],
  "container-title": "Gene",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0378111900004315?httpAccept=text/xml",
      "content-type": "text/xml",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0378111900004315?httpAccept=text/plain",
      "content-type": "text/plain",
      "content-version": "vor",
      "intended-application": "text-mining"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        4,
        10
      ]
    ],
    "date-time": "2023-04-10T22:43:26Z",
    "timestamp": 1681166606000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0378111900004315"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2000,
        12
      ]
    ]
  },
  "references-count": 16,
  "journal-issue": {
    "issue": "1-2",
    "published-print": {
      "date-parts": [
        [
          2000,
          12
        ]
      ]
    }
  },
  "alternative-id": [
    "S0378111900004315"
  ],
  "URL": "http://dx.doi.org/10.1016/S0378-1119(00)00431-5",
  "relation": {},
  "ISSN": [
    "0378-1119"
  ],
  "subject": [],
  "container-title-short": "Gene",
  "published": {
    "date-parts": [
      [
        2000,
        12
      ]
    ]
  }
}