{"id":"https://openalex.org/W2275721306","doi":"https://doi.org/10.1093/database/baw005","title":"EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation","display_name":"EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2275721306","doi":"https://doi.org/10.1093/database/baw005","mag":"2275721306","pmid":"https://pubmed.ncbi.nlm.nih.gov/26896844"},"language":"en","primary_location":{"id":"doi:10.1093/database/baw005","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw005","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw005/8222692/baw005.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw005/8222692/baw005.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025850900","display_name":"Evangelos Pafilis","orcid":"https://orcid.org/0000-0001-5079-0125"},"institutions":[{"id":"https://openalex.org/I4210131924","display_name":"Hellenic Centre for Marine Research","ror":"https://ror.org/038kffh84","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210131924"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Evangelos Pafilis","raw_affiliation_strings":["Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece, pafilis@hcmr.gr","Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece,"],"affiliations":[{"raw_affiliation_string":"Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece, pafilis@hcmr.gr","institution_ids":[]},{"raw_affiliation_string":"Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece,","institution_ids":["https://openalex.org/I4210131924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091806083","display_name":"Pier Luigi Buttigieg","orcid":"https://orcid.org/0000-0002-4366-3088"},"institutions":[{"id":"https://openalex.org/I127251866","display_name":"Alfred-Wegener-Institut Helmholtz-Zentrum f\u00fcr Polar- und Meeresforschung","ror":"https://ror.org/032e6b942","country_code":"DE","type":"facility","lineage":["https://openalex.org/I127251866","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Pier Luigi Buttigieg","raw_affiliation_strings":["Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, Germany","Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, Germany,"],"affiliations":[{"raw_affiliation_string":"Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, Germany","institution_ids":["https://openalex.org/I127251866"]},{"raw_affiliation_string":"Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, Germany,","institution_ids":["https://openalex.org/I127251866"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029560442","display_name":"Barbra D. Ferrell","orcid":"https://orcid.org/0000-0003-3057-3478"},"institutions":[{"id":"https://openalex.org/I1312106833","display_name":"Biotechnology Institute","ror":"https://ror.org/00s1jty20","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312106833"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Barbra Ferrell","raw_affiliation_strings":["Delaware Biotechnology Institute, Newark, DE 19711, Delaware, USA","Delaware Biotechnology Institute, Newark, DE 19711, Delaware, USA,"],"affiliations":[{"raw_affiliation_string":"Delaware Biotechnology Institute, Newark, DE 19711, Delaware, USA","institution_ids":[]},{"raw_affiliation_string":"Delaware Biotechnology Institute, Newark, DE 19711, Delaware, USA,","institution_ids":["https://openalex.org/I1312106833"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013661164","display_name":"Emiliano Pereira-Flores","orcid":"https://orcid.org/0000-0001-5830-3328"},"institutions":[{"id":"https://openalex.org/I4210103014","display_name":"Max Planck Institute for Marine Microbiology","ror":"https://ror.org/02385fa51","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210103014"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Emiliano Pereira","raw_affiliation_strings":["Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany","Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany,"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany","institution_ids":["https://openalex.org/I4210103014"]},{"raw_affiliation_string":"Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany,","institution_ids":["https://openalex.org/I4210103014"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068746140","display_name":"Julia Schnetzer","orcid":null},"institutions":[{"id":"https://openalex.org/I193619901","display_name":"Constructor University","ror":"https://ror.org/02yrs2n53","country_code":"DE","type":"education","lineage":["https://openalex.org/I193619901"]},{"id":"https://openalex.org/I4210103014","display_name":"Max Planck Institute for Marine Microbiology","ror":"https://ror.org/02385fa51","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210103014"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Julia Schnetzer","raw_affiliation_strings":["Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Campus Ring 1, 28759, Bremen, Germany, and","Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany,","Jacobs University gGmbH, School of Engineering and Sciences, Campus Ring 1, 28759, Bremen, Germany, and"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Campus Ring 1, 28759, Bremen, Germany, and","institution_ids":[]},{"raw_affiliation_string":"Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany,","institution_ids":["https://openalex.org/I4210103014"]},{"raw_affiliation_string":"Jacobs University gGmbH, School of Engineering and Sciences, Campus Ring 1, 28759, Bremen, Germany, and","institution_ids":["https://openalex.org/I193619901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091671086","display_name":"Christos Arvanitidis","orcid":"https://orcid.org/0000-0002-6924-5255"},"institutions":[{"id":"https://openalex.org/I4210131924","display_name":"Hellenic Centre for Marine Research","ror":"https://ror.org/038kffh84","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210131924"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Christos Arvanitidis","raw_affiliation_strings":["Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece","Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece,"],"affiliations":[{"raw_affiliation_string":"Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece","institution_ids":["https://openalex.org/I4210131924"]},{"raw_affiliation_string":"Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece,","institution_ids":["https://openalex.org/I4210131924"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005772961","display_name":"Lars Juhl Jensen","orcid":"https://orcid.org/0000-0001-7885-715X"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Lars Juhl Jensen","raw_affiliation_strings":["Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark pafilis@hcmr.gr","Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark pafilis@hcmr.gr","institution_ids":[]},{"raw_affiliation_string":"Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5025850900"],"corresponding_institution_ids":["https://openalex.org/I4210131924"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":3.5565,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.92854409,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"2016","issue":null,"first_page":"baw005","last_page":"baw005"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9854999780654907,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.8916686177253723},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7910047769546509},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7880133986473083},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7156934142112732},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.6906460523605347},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.6337031722068787},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5826448202133179},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.5037309527397156},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4862052798271179},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19741347432136536},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1338198482990265},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.103168785572052},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.07666966319084167}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.8916686177253723},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7910047769546509},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7880133986473083},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7156934142112732},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.6906460523605347},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.6337031722068787},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5826448202133179},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.5037309527397156},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4862052798271179},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19741347432136536},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1338198482990265},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.103168785572052},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.07666966319084167},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004463","descriptor_name":"Ecology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004463","descriptor_name":"Ecology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004463","descriptor_name":"Ecology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/database/baw005","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw005","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw005/8222692/baw005.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:26896844","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26896844","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:epic.awi.de:43662","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400378","display_name":"Helmholtz-Zentrum f\u00fcr Polar-und Meeresforschung (Alfred-Wegener-Institut)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2799732068","host_organization_name":"Royal Prince Alfred Hospital","host_organization_lineage":["https://openalex.org/I2799732068"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:osti.gov:1253360","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1253360","pdf_url":"https://www.osti.gov/servlets/purl/1253360","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:open-archive.highwire.org:databa:2016/0/baw005","is_oa":false,"landing_page_url":"http://database.oxfordjournals.org/cgi/content/short/2016/0/baw005","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4761108","is_oa":true,"landing_page_url":"http://doi.org/10.1093/database/baw005","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/9b544ee4-c6aa-46e3-8d83-2895c51628c5","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/9b544ee4-c6aa-46e3-8d83-2895c51628c5","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Pafilis , E , Buttigieg , P L , Ferrell , B , Pereira , E , Schnetzer , J , Arvanitidis , C & Jensen , L J 2016 , ' EXTRACT : interactive extraction of environment metadata and term suggestion for metagenomic sample annotation ' , Database: The Journal of Biological Databases and Curation , vol. 2016 , baw005 . https://doi.org/10.1093/database/baw005","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/database/baw005","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw005","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw005/8222692/baw005.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320321917","display_name":"General Secretariat for Research and Technology","ror":"https://ror.org/04yeh8h63"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2275721306.pdf","grobid_xml":"https://content.openalex.org/works/W2275721306.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1577541759","https://openalex.org/W1700570096","https://openalex.org/W1982265452","https://openalex.org/W1987522618","https://openalex.org/W2010798628","https://openalex.org/W2024038403","https://openalex.org/W2053039860","https://openalex.org/W2054720302","https://openalex.org/W2071879021","https://openalex.org/W2074640468","https://openalex.org/W2074955520","https://openalex.org/W2097877306","https://openalex.org/W2100627415","https://openalex.org/W2103017472","https://openalex.org/W2116034137","https://openalex.org/W2122402213","https://openalex.org/W2123579157","https://openalex.org/W2124045889","https://openalex.org/W2124282646","https://openalex.org/W2127546476","https://openalex.org/W2142016317","https://openalex.org/W2146089916","https://openalex.org/W2146679517","https://openalex.org/W2149852578","https://openalex.org/W2160259754","https://openalex.org/W2166240318","https://openalex.org/W2168644196","https://openalex.org/W6634409857"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W2058118494","https://openalex.org/W2392768766","https://openalex.org/W4388282505"],"abstract_inverted_index":{"The":[0,83],"microbial":[1],"and":[2,30,50,59,80,101,112,115,122,133],"molecular":[3],"ecology":[4],"research":[5],"communities":[6],"have":[7,38,142],"made":[8],"substantial":[9],"progress":[10],"on":[11],"developing":[12],"standards":[13],"for":[14,54,72],"annotating":[15],"samples":[16],"with":[17,33],"environment":[18,116],"metadata.":[19],"However,":[20],"sample":[21],"manual":[22,121],"annotation":[23,43,55,130],"is":[24],"a":[25],"highly":[26],"labor":[27],"intensive":[28],"process":[29],"requires":[31],"familiarity":[32],"the":[34,67,86,93],"terminologies":[35],"used.":[36],"We":[37],"therefore":[39],"developed":[40],"an":[41],"interactive":[42],"tool,":[44],"EXTRACT,":[45],"which":[46],"helps":[47,134],"curators":[48,135],"identify":[49],"extract":[51],"standard-compliant":[52],"terms":[53,138],"of":[56,76,119],"metagenomic":[57],"records":[58],"other":[60],"samples.":[61],"Behind":[62],"its":[63],"web-based":[64],"user":[65],"interface,":[66],"system":[68,94],"combines":[69],"published":[70],"methods":[71],"named":[73],"entity":[74],"recognition":[75],"environment,":[77],"organism,":[78],"tissue":[79],"disease":[81],"terms.":[82,117],"evaluators":[84],"in":[85,107],"BioCreative":[87],"V":[88],"Interactive":[89],"Annotation":[90],"Task":[91],"found":[92],"to":[95,104,136],"be":[96,105],"intuitive,":[97],"useful,":[98],"well":[99],"documented":[100],"sufficiently":[102],"accurate":[103],"helpful":[106],"spotting":[108],"relevant":[109],"text":[110],"passages":[111],"extracting":[113],"organism":[114],"Comparison":[118],"fully":[120],"text-mining-assisted":[123],"curation":[124],"revealed":[125],"that":[126,139],"EXTRACT":[127],"speeds":[128],"up":[129],"by":[131],"15-25%":[132],"detect":[137],"would":[140],"otherwise":[141],"been":[143],"missed.":[144],"Database":[145],"URL:":[146],"https://extract.hcmr.gr/.":[147]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":10}],"updated_date":"2026-03-08T08:50:53.379069","created_date":"2025-10-10T00:00:00"}
