{"id":"https://openalex.org/W6912774572","doi":"https://doi.org/10.5281/zenodo.7438209","title":"Text mining pipelines for the extraction of biological entities","display_name":"Text mining pipelines for the extraction of biological entities","publication_year":2022,"publication_date":"2022-12-14","ids":{"openalex":"https://openalex.org/W6912774572","doi":"https://doi.org/10.5281/zenodo.7438209"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:7438209","is_oa":true,"landing_page_url":"https://zenodo.org/record/7438209","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/7438209","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"L\u00f6ffler, Felicitas","orcid":"https://orcid.org/0000-0001-6423-7427"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"L\u00f6ffler, Felicitas","raw_affiliation_strings":["Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Shafiei, Fateme","orcid":"https://orcid.org/0000-0001-9731-9496"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Shafiei, Fateme","raw_affiliation_strings":["Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Witte, Ren\u00e9","orcid":"https://orcid.org/0000-0002-4833-075X"},"institutions":[{"id":"https://openalex.org/I60158472","display_name":"Concordia University","ror":"https://ror.org/0420zvk78","country_code":"CA","type":"education","lineage":["https://openalex.org/I60158472"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Witte, Ren\u00e9","raw_affiliation_strings":["Semantic Software Lab, Concordia University Montr\u00e9al, Canada"],"affiliations":[{"raw_affiliation_string":"Semantic Software Lab, Concordia University Montr\u00e9al, Canada","institution_ids":["https://openalex.org/I60158472"]}]},{"author_position":"middle","author":{"id":null,"display_name":"K\u00f6nig-Ries, Birgitta","orcid":"https://orcid.org/0000-0002-2382-9722"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"K\u00f6nig-Ries, Birgitta","raw_affiliation_strings":["Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"last","author":{"id":null,"display_name":"Klan, Friederike","orcid":"https://orcid.org/0000-0002-1856-7334"},"institutions":[{"id":"https://openalex.org/I2898391981","display_name":"Deutsches Zentrum f\u00fcr Luft- und Raumfahrt e. V. (DLR)","ror":"https://ror.org/04bwf3e34","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I2898391981"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Klan, Friederike","raw_affiliation_strings":["Data Acquistion and Mobilization Department, Institute of Data Science, German Aerospace Center (DLR), Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Data Acquistion and Mobilization Department, Institute of Data Science, German Aerospace Center (DLR), Jena, Germany","institution_ids":["https://openalex.org/I2898391981"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I76198965"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.6726999878883362},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.6466000080108643},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.612500011920929},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.48030000925064087},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.47909998893737793},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.46799999475479126},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.4251999855041504}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7581999897956848},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.6726999878883362},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.6466000080108643},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.612500011920929},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.551800012588501},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.48030000925064087},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.47909998893737793},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.46799999475479126},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.4251999855041504},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37540000677108765},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.3321000039577484},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.3154999911785126},{"id":"https://openalex.org/C2777946921","wikidata":"https://www.wikidata.org/wiki/Q7449044","display_name":"Semantic analysis (machine learning)","level":2,"score":0.295199990272522},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.2888000011444092},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.2870999872684479},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.28119999170303345},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27880001068115234},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.2705000042915344},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.26969999074935913},{"id":"https://openalex.org/C197046077","wikidata":"https://www.wikidata.org/wiki/Q785337","display_name":"Web mining","level":3,"score":0.26420000195503235},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.26089999079704285},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.2606000006198883}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:7438209","is_oa":true,"landing_page_url":"https://zenodo.org/record/7438209","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},{"id":"doi:10.5281/zenodo.7438209","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.7438209","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:7438209","is_oa":true,"landing_page_url":"https://zenodo.org/record/7438209","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"We":[0,27],"provide":[1],"two":[2],"text":[3],"mining":[4],"pipelines":[5,19,23,30,74],"developed":[6],"with":[7,35],"the":[8,21,29,53],"GATE":[9],"framework":[10],"to":[11,31,71,75,80,82],"extract":[12],"biological":[13,55,77],"entities":[14],"from":[15,37,45,90],"textual":[16,33],"resources.<br>":[17],"Both":[18],"utilize":[20],"existing":[22],"[OrganismTagger](http://dx.doi.org/10.1093/bioinformatics/btr452)":[24],"and":[25,40,79],"[BiodivTagger](https://aclanthology.org/2020.lrec-1.560.pdf).":[26],"extended":[28],"annotate":[32,76],"information":[34,68],"URIs":[36],"knowledge":[38],"bases":[39],"further":[41],"semantic":[42,85],"relations":[43],"obtained":[44,89],"hierarchy":[46],"relationships.":[47],"1.":[48],"BiodivTagger":[49],"pipeline:":[50,63],"extraction":[51,64],"of":[52,65],"following":[54],"entities:":[56],"Material,":[57],"Process,":[58],"Environment,":[59],"Quality":[60],"2.":[61],"OrganismTagger":[62],"Organisms":[66],"Further":[67],"on":[69],"how":[70,81],"use":[72],"these":[73],"data":[78],"create":[83],"a":[84],"index":[86],"can":[87],"be":[88],"our":[91],"related":[92],"GitHub":[93],"repository:":[94],"https://github.com/fusion-jena/semantic-search-usability-analysis/":[95]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
