{"id":"https://openalex.org/W2903305690","doi":"https://doi.org/10.1186/s13321-018-0312-9","title":"MER: a shell script and annotation server for minimal named entity recognition and linking","display_name":"MER: a shell script and annotation server for minimal named entity recognition and linking","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2903305690","doi":"https://doi.org/10.1186/s13321-018-0312-9","mag":"2903305690","pmid":"https://pubmed.ncbi.nlm.nih.gov/30519990"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-018-0312-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0312-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0312-9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0312-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014333753","display_name":"Francisco M. Couto","orcid":"https://orcid.org/0000-0003-0627-1496"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Francisco M. Couto","raw_affiliation_strings":["LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749 016, Lisbon, Portugal. fcouto@di.fc.ul.pt","LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749 016, Lisbon, Portugal"],"affiliations":[{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749 016, Lisbon, Portugal. fcouto@di.fc.ul.pt","institution_ids":["https://openalex.org/I141596103"]},{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749 016, Lisbon, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024583659","display_name":"Andr\u00e9 Lam\u00farias","orcid":null},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Andre Lamurias","raw_affiliation_strings":["Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, 1749 016, Lisbon, Portugal","LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749 016, Lisbon, Portugal"],"affiliations":[{"raw_affiliation_string":"Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, 1749 016, Lisbon, Portugal","institution_ids":["https://openalex.org/I141596103"]},{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749 016, Lisbon, Portugal","institution_ids":["https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5014333753"],"corresponding_institution_ids":["https://openalex.org/I141596103"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.9787,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.92340689,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"58","last_page":"58"},"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/T10028","display_name":"Topic Modeling","score":0.9965000152587891,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9922999739646912,"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/computer-science","display_name":"Computer science","score":0.9028825163841248},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6807700395584106},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5697226524353027},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.4821007549762726},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.43421247601509094},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.4265063405036926},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35518670082092285},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3411528170108795},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.3051551580429077},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2753671407699585},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.22122696042060852},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.16274327039718628}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.9028825163841248},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6807700395584106},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5697226524353027},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.4821007549762726},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.43421247601509094},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.4265063405036926},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35518670082092285},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3411528170108795},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.3051551580429077},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2753671407699585},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.22122696042060852},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.16274327039718628},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-018-0312-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0312-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0312-9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:30519990","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30519990","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:8f24c49891964eabb65b3420b1fcb125","is_oa":true,"landing_page_url":"https://doaj.org/article/8f24c49891964eabb65b3420b1fcb125","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":"Journal of Cheminformatics, Vol 10, Iss 1, Pp 1-10 (2018)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6755715","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6755715","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":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-018-0312-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0312-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0312-9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.6399999856948853}],"awards":[{"id":"https://openalex.org/G1820475556","display_name":null,"funder_award_id":"PD/BD/106083/2015","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4384961418","display_name":null,"funder_award_id":"PTDC/CCI-BIO/28685/2017","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5454278309","display_name":null,"funder_award_id":"/2017","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6128949145","display_name":null,"funder_award_id":"UID/CEC/00408/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6299983296","display_name":null,"funder_award_id":"PTDC/","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7540450269","display_name":null,"funder_award_id":"ID/MULTI/04046/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2903305690.pdf","grobid_xml":"https://content.openalex.org/works/W2903305690.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1967096360","https://openalex.org/W2020278455","https://openalex.org/W2028041302","https://openalex.org/W2033377040","https://openalex.org/W2037589601","https://openalex.org/W2076632311","https://openalex.org/W2077327925","https://openalex.org/W2096525273","https://openalex.org/W2096953947","https://openalex.org/W2099964107","https://openalex.org/W2103126992","https://openalex.org/W2106797966","https://openalex.org/W2119613819","https://openalex.org/W2123152121","https://openalex.org/W2124045889","https://openalex.org/W2143742443","https://openalex.org/W2149369282","https://openalex.org/W2165644686","https://openalex.org/W2170282111","https://openalex.org/W2205496875","https://openalex.org/W2275721306","https://openalex.org/W2281036777","https://openalex.org/W2515403501","https://openalex.org/W2525741381","https://openalex.org/W2558999090","https://openalex.org/W2604808360","https://openalex.org/W2610394652","https://openalex.org/W2611349437","https://openalex.org/W2767470330","https://openalex.org/W2767683865","https://openalex.org/W2769714647","https://openalex.org/W2790457751","https://openalex.org/W2792330846","https://openalex.org/W2904867915","https://openalex.org/W2952769172","https://openalex.org/W4229004063"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2033889310","https://openalex.org/W644889988","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2086577855","https://openalex.org/W2218034408","https://openalex.org/W1575418055","https://openalex.org/W2392921965","https://openalex.org/W4377865234"],"abstract_inverted_index":{"Named-entity":[0],"recognition":[1,34,130],"aims":[2],"at":[3],"identifying":[4],"the":[5,61,66,88,100,112,118,152],"fragments":[6],"of":[7,12,63,68,107,117,157,161,188],"text":[8,119],"that":[9,14,167],"mention":[10],"entities":[11,25,67],"interest,":[13],"afterwards":[15],"could":[16],"be":[17],"linked":[18],"to":[19,143,194],"a":[20,49,56,72,77,84,127,136,195,219,227],"knowledge":[21],"base":[22],"where":[23,95],"those":[24],"are":[26],"described.":[27],"This":[28],"manuscript":[29],"presents":[30],"our":[31,168],"minimal":[32],"named-entity":[33],"and":[35,43,83,102,115,124,126,149,155,175,212,225],"linking":[36],"tool":[37],"(MER),":[38],"designed":[39],"with":[40,60,76],"flexibility,":[41],"autonomy":[42],"efficiency":[44,106],"in":[45,135,151,177,205,210,218],"mind.":[46],"To":[47],"annotate":[48],"given":[50],"text,":[51],"MER":[52,96,108,132,190,214],"only":[53,204],"requires:":[54],"(1)":[55],"lexicon":[57,101],"(text":[58,173],"file)":[59],"list":[62],"terms":[64],"representing":[65],"interest;":[69],"(2)":[70],"optionally":[71],"tab-separated":[73],"values":[74],"file":[75],"link":[78],"for":[79],"each":[80,171],"term;":[81],"(3)":[82],"Unix":[85],"shell.":[86],"Alternatively,":[87],"user":[89],"can":[90],"provide":[91],"an":[92,146],"ontology":[93],"from":[94,110],"will":[97],"automatically":[98],"generate":[99],"links":[103],"files.":[104],"The":[105,164],"derives":[109],"exploring":[111],"high":[113],"performance":[114,207],"reliability":[116],"processing":[120],"command-line":[121],"tools":[122],"grep":[123],"awk,":[125],"novel":[128],"inverted":[129],"technique.":[131],"was":[133,191],"deployed":[134],"cloud":[137],"infrastructure":[138],"using":[139,185],"multiple":[140],"Virtual":[141],"Machines":[142],"work":[144],"as":[145],"annotation":[147,158],"server":[148],"participate":[150],"Technical":[153],"Interoperability":[154],"Performance":[156],"Servers":[159],"task":[160],"BioCreative":[162],"V.5.":[163],"results":[165,202],"show":[166],"solution":[169,199],"processed":[170],"document":[172],"retrieval":[174],"annotation)":[176],"less":[178],"than":[179],"3":[180],"s":[181],"on":[182],"average":[183],"without":[184],"any":[186],"type":[187],"cache.":[189],"also":[192,209],"compared":[193],"state-of-the-art":[196],"dictionary":[197],"lookup":[198],"obtaining":[200],"competitive":[201],"not":[203],"computational":[206],"but":[208],"precision":[211],"recall.":[213],"is":[215],"publicly":[216],"available":[217],"GitHub":[220],"repository":[221],"(":[222,231],"https://github.com/lasigeBioTM/MER":[223],")":[224],"through":[226],"RESTful":[228],"Web":[229],"service":[230],"http://labs.fc.ul.pt/mer/":[232],").":[233]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
