{"id":"https://openalex.org/W3113537210","doi":"https://doi.org/10.1186/s12859-020-03894-8","title":"A2A: a platform for research in biomedical literature search","display_name":"A2A: a platform for research in biomedical literature search","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3113537210","doi":"https://doi.org/10.1186/s12859-020-03894-8","mag":"3113537210","pmid":"https://pubmed.ncbi.nlm.nih.gov/33349237"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03894-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03894-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03894-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03894-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002115688","display_name":"Maciej Rybi\u0144ski","orcid":"https://orcid.org/0000-0002-0174-0567"},"institutions":[{"id":"https://openalex.org/I42894916","display_name":"Data61","ror":"https://ror.org/03q397159","country_code":"AU","type":"other","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I42894916","https://openalex.org/I4387156119"]},{"id":"https://openalex.org/I1292875679","display_name":"Commonwealth Scientific and Industrial Research Organisation","ror":"https://ror.org/03qn8fb07","country_code":"AU","type":"funder","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Maciej Rybinski","raw_affiliation_strings":["CSIRO Data61, Sydney, Australia. maciek.rybinski@csiro.au","CSIRO Data61, Sydney, Australia"],"affiliations":[{"raw_affiliation_string":"CSIRO Data61, Sydney, Australia. maciek.rybinski@csiro.au","institution_ids":[]},{"raw_affiliation_string":"CSIRO Data61, Sydney, Australia","institution_ids":["https://openalex.org/I42894916","https://openalex.org/I1292875679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041251183","display_name":"Sarvnaz Karimi","orcid":"https://orcid.org/0000-0002-4927-3937"},"institutions":[{"id":"https://openalex.org/I42894916","display_name":"Data61","ror":"https://ror.org/03q397159","country_code":"AU","type":"other","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I42894916","https://openalex.org/I4387156119"]},{"id":"https://openalex.org/I1292875679","display_name":"Commonwealth Scientific and Industrial Research Organisation","ror":"https://ror.org/03qn8fb07","country_code":"AU","type":"funder","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Sarvnaz Karimi","raw_affiliation_strings":["CSIRO Data61, Sydney, Australia"],"affiliations":[{"raw_affiliation_string":"CSIRO Data61, Sydney, Australia","institution_ids":["https://openalex.org/I42894916","https://openalex.org/I1292875679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083515958","display_name":"Vincent Nguyen","orcid":"https://orcid.org/0000-0003-3744-1523"},"institutions":[{"id":"https://openalex.org/I1292875679","display_name":"Commonwealth Scientific and Industrial Research Organisation","ror":"https://ror.org/03qn8fb07","country_code":"AU","type":"funder","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I4387156119"]},{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]},{"id":"https://openalex.org/I42894916","display_name":"Data61","ror":"https://ror.org/03q397159","country_code":"AU","type":"other","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I42894916","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Vincent Nguyen","raw_affiliation_strings":["Australian National University, Canberra, Australia","CSIRO Data61, Sydney, Australia"],"affiliations":[{"raw_affiliation_string":"Australian National University, Canberra, Australia","institution_ids":["https://openalex.org/I118347636"]},{"raw_affiliation_string":"CSIRO Data61, Sydney, Australia","institution_ids":["https://openalex.org/I42894916","https://openalex.org/I1292875679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077002072","display_name":"C\u00e9cile Paris","orcid":"https://orcid.org/0000-0003-3816-0176"},"institutions":[{"id":"https://openalex.org/I42894916","display_name":"Data61","ror":"https://ror.org/03q397159","country_code":"AU","type":"other","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I42894916","https://openalex.org/I4387156119"]},{"id":"https://openalex.org/I1292875679","display_name":"Commonwealth Scientific and Industrial Research Organisation","ror":"https://ror.org/03qn8fb07","country_code":"AU","type":"funder","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Cecile Paris","raw_affiliation_strings":["CSIRO Data61, Sydney, Australia"],"affiliations":[{"raw_affiliation_string":"CSIRO Data61, Sydney, Australia","institution_ids":["https://openalex.org/I42894916","https://openalex.org/I1292875679"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5002115688"],"corresponding_institution_ids":["https://openalex.org/I1292875679","https://openalex.org/I42894916"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.3338,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.58457616,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"21","issue":"S19","first_page":"572","last_page":"572"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10028","display_name":"Topic Modeling","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7858313322067261},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7718176245689392},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.7118481397628784},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5509719252586365},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.5412260293960571},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5061694979667664},{"id":"https://openalex.org/keywords/query-expansion","display_name":"Query expansion","score":0.46162325143814087},{"id":"https://openalex.org/keywords/controlled-vocabulary","display_name":"Controlled vocabulary","score":0.4485616683959961},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3232889175415039}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7858313322067261},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7718176245689392},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.7118481397628784},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5509719252586365},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.5412260293960571},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5061694979667664},{"id":"https://openalex.org/C99016210","wikidata":"https://www.wikidata.org/wiki/Q5488129","display_name":"Query expansion","level":2,"score":0.46162325143814087},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.4485616683959961},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3232889175415039},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-020-03894-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03894-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03894-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33349237","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33349237","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:c93d35efb04f4dd58a7b31fdac029e10","is_oa":true,"landing_page_url":"https://doaj.org/article/c93d35efb04f4dd58a7b31fdac029e10","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss S19, Pp 1-27 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7751125","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7751125","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03894-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03894-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03894-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.6000000238418579}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320386","display_name":"Commonwealth Scientific and Industrial Research Organisation","ror":"https://ror.org/03qn8fb07"},{"id":"https://openalex.org/F4320320972","display_name":"RMIT University","ror":"https://ror.org/04ttjf776"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3113537210.pdf","grobid_xml":"https://content.openalex.org/works/W3113537210.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W45944204","https://openalex.org/W100892167","https://openalex.org/W1845198550","https://openalex.org/W1980199609","https://openalex.org/W2006996936","https://openalex.org/W2050930276","https://openalex.org/W2052201263","https://openalex.org/W2105157020","https://openalex.org/W2114453188","https://openalex.org/W2115536324","https://openalex.org/W2153252192","https://openalex.org/W2169213601","https://openalex.org/W2396881363","https://openalex.org/W2412389409","https://openalex.org/W2511654892","https://openalex.org/W2604599254","https://openalex.org/W2605213733","https://openalex.org/W2739802412","https://openalex.org/W2740321901","https://openalex.org/W2740744325","https://openalex.org/W2792556718","https://openalex.org/W2799149544","https://openalex.org/W2887689483","https://openalex.org/W2946979871","https://openalex.org/W2947054861","https://openalex.org/W2953926227","https://openalex.org/W2955714298","https://openalex.org/W3013322209","https://openalex.org/W3013617309","https://openalex.org/W3013638393","https://openalex.org/W3021052948","https://openalex.org/W3032541190","https://openalex.org/W3104055892","https://openalex.org/W4246858749","https://openalex.org/W4288086540","https://openalex.org/W4288280763"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2770764537","https://openalex.org/W2160726690"],"abstract_inverted_index":{"We":[0,26],"introduce":[1],"the":[2,13],"A2A":[3],"search":[4,20],"and":[5,32],"benchmarking":[6],"tool":[7],"which":[8],"is":[9],"publicly":[10],"available":[11],"for":[12,40],"researchers":[14],"who":[15],"want":[16],"to":[17,48],"explore":[18],"different":[19],"strategies":[21,31],"over":[22],"published":[23],"biomedical":[24],"literature.":[25],"outline":[27],"several":[28],"query":[29],"formulation":[30],"present":[33],"their":[34],"evaluations":[35],"with":[36],"known":[37],"human":[38],"judgements":[39],"a":[41],"large":[42],"pool":[43],"of":[44],"topics,":[45],"from":[46],"genomics":[47],"precision":[49],"medicine.":[50]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}