{"id":"https://openalex.org/W4281710388","doi":"https://doi.org/10.1186/s13321-022-00610-x","title":"Chemical reaction network knowledge graphs: the OntoRXN ontology","display_name":"Chemical reaction network knowledge graphs: the OntoRXN ontology","publication_year":2022,"publication_date":"2022-05-30","ids":{"openalex":"https://openalex.org/W4281710388","doi":"https://doi.org/10.1186/s13321-022-00610-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/35637523"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-022-00610-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00610-x","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00610-x","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/counter/pdf/10.1186/s13321-022-00610-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003060160","display_name":"Diego Garay\u2010Ruiz","orcid":"https://orcid.org/0000-0003-0744-0562"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]},{"id":"https://openalex.org/I4210088955","display_name":"Institut Catal\u00e0 d'Investigaci\u00f3 Qu\u00edmica","ror":"https://ror.org/013j2zh96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210088955","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Diego Garay-Ruiz","raw_affiliation_strings":["Departament de Qu\u00edmica F\u00edsica i Inorg\u00e0nica, Universitat Rovira i Virgili, Marcel . l\u00ed Domingo s/n, 43007, Tarragona, Spain","Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Pa\u00efsos Catalans 16, 43007, Tarragona, Spain"],"affiliations":[{"raw_affiliation_string":"Departament de Qu\u00edmica F\u00edsica i Inorg\u00e0nica, Universitat Rovira i Virgili, Marcel . l\u00ed Domingo s/n, 43007, Tarragona, Spain","institution_ids":["https://openalex.org/I55952717"]},{"raw_affiliation_string":"Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Pa\u00efsos Catalans 16, 43007, Tarragona, Spain","institution_ids":["https://openalex.org/I4210088955"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011694384","display_name":"Carles B\u00f3","orcid":"https://orcid.org/0000-0001-9581-2922"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]},{"id":"https://openalex.org/I4210088955","display_name":"Institut Catal\u00e0 d'Investigaci\u00f3 Qu\u00edmica","ror":"https://ror.org/013j2zh96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210088955","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Carles Bo","raw_affiliation_strings":["Departament de Qu\u00edmica F\u00edsica i Inorg\u00e0nica, Universitat Rovira i Virgili, Marcel . l\u00ed Domingo s/n, 43007, Tarragona, Spain. cbo@iciq.cat","Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Pa\u00efsos Catalans 16, 43007, Tarragona, Spain. cbo@iciq.cat","Departament de Qu\u00edmica F\u00edsica i Inorg\u00e0nica, Universitat Rovira i Virgili, Marcel . l\u00ed Domingo s/n, 43007, Tarragona, Spain","Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Pa\u00efsos Catalans 16, 43007, Tarragona, Spain"],"affiliations":[{"raw_affiliation_string":"Departament de Qu\u00edmica F\u00edsica i Inorg\u00e0nica, Universitat Rovira i Virgili, Marcel . l\u00ed Domingo s/n, 43007, Tarragona, Spain. cbo@iciq.cat","institution_ids":[]},{"raw_affiliation_string":"Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Pa\u00efsos Catalans 16, 43007, Tarragona, Spain. cbo@iciq.cat","institution_ids":[]},{"raw_affiliation_string":"Departament de Qu\u00edmica F\u00edsica i Inorg\u00e0nica, Universitat Rovira i Virgili, Marcel . l\u00ed Domingo s/n, 43007, Tarragona, Spain","institution_ids":["https://openalex.org/I55952717"]},{"raw_affiliation_string":"Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Pa\u00efsos Catalans 16, 43007, Tarragona, Spain","institution_ids":["https://openalex.org/I4210088955"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003060160"],"corresponding_institution_ids":["https://openalex.org/I4210088955","https://openalex.org/I55952717"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.1041,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.88586261,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"14","issue":"1","first_page":"29","last_page":"29"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9950000047683716,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9879999756813049,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials 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":0.8603965044021606},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6729713678359985},{"id":"https://openalex.org/keywords/tree-traversal","display_name":"Tree traversal","score":0.5726277828216553},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5649242401123047},{"id":"https://openalex.org/keywords/sparql","display_name":"SPARQL","score":0.5189716219902039},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5000622272491455},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.429864764213562},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.40514233708381653},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.3744164705276489},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.3673946261405945},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.19482427835464478},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.12633076310157776}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8603965044021606},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6729713678359985},{"id":"https://openalex.org/C140745168","wikidata":"https://www.wikidata.org/wiki/Q1210082","display_name":"Tree traversal","level":2,"score":0.5726277828216553},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5649242401123047},{"id":"https://openalex.org/C41009113","wikidata":"https://www.wikidata.org/wiki/Q54871","display_name":"SPARQL","level":4,"score":0.5189716219902039},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5000622272491455},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.429864764213562},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.40514233708381653},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.3744164705276489},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.3673946261405945},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.19482427835464478},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.12633076310157776},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-022-00610-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00610-x","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00610-x","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:35637523","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35637523","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:027153f147b644e68856e200d3fd536d","is_oa":true,"landing_page_url":"https://doaj.org/article/027153f147b644e68856e200d3fd536d","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 14, Iss 1, Pp 1-12 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9153116","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9153116","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/s13321-022-00610-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00610-x","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00610-x","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":[],"awards":[{"id":"https://openalex.org/G3146262949","display_name":null,"funder_award_id":"PID2020-112806RB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320334830","display_name":"Ag\u00e8ncia de Gesti\u00f3 d'Ajuts Universitaris i de Recerca","ror":"https://ror.org/01n4pqe45"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4281710388.pdf","grobid_xml":"https://content.openalex.org/works/W4281710388.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1899191765","https://openalex.org/W2006026068","https://openalex.org/W2023902342","https://openalex.org/W2029812252","https://openalex.org/W2033377040","https://openalex.org/W2033774898","https://openalex.org/W2047600440","https://openalex.org/W2053014304","https://openalex.org/W2053778958","https://openalex.org/W2064270057","https://openalex.org/W2102653059","https://openalex.org/W2103017472","https://openalex.org/W2110279208","https://openalex.org/W2134697397","https://openalex.org/W2137079713","https://openalex.org/W2143198425","https://openalex.org/W2216357933","https://openalex.org/W2295556250","https://openalex.org/W2518156262","https://openalex.org/W2563593663","https://openalex.org/W2807665686","https://openalex.org/W2897326591","https://openalex.org/W2932332855","https://openalex.org/W2947398416","https://openalex.org/W2994738957","https://openalex.org/W3003213525","https://openalex.org/W3012638926","https://openalex.org/W3093066640","https://openalex.org/W3112600195","https://openalex.org/W3160452578","https://openalex.org/W3164149563","https://openalex.org/W3170771812","https://openalex.org/W3190198842","https://openalex.org/W3211718555","https://openalex.org/W4206181733","https://openalex.org/W4210318910","https://openalex.org/W4221016472","https://openalex.org/W4239696231","https://openalex.org/W4245861846","https://openalex.org/W4254697110"],"related_works":["https://openalex.org/W2615202182","https://openalex.org/W4206665951","https://openalex.org/W3085073370","https://openalex.org/W2904139343","https://openalex.org/W2529794967","https://openalex.org/W2604011835","https://openalex.org/W2978246852","https://openalex.org/W2295924417","https://openalex.org/W4241483715","https://openalex.org/W4243630814"],"abstract_inverted_index":{"The":[0],"organization":[1],"and":[2,45,99,117,126,178],"management":[3],"of":[4,7,18,39,167,175,183],"large":[5],"amounts":[6],"data":[8],"has":[9],"become":[10],"a":[11,27,42,57,88],"major":[12],"point":[13],"in":[14,128,137],"almost":[15],"all":[16],"areas":[17],"human":[19],"knowledge.":[20],"In":[21,51],"this":[22,52],"context,":[23],"semantic":[24,169],"approaches":[25],"propose":[26,87],"structure":[28,91],"for":[29,103,147],"the":[30,37,61,100,104,114,119,143,155,165,168,173,181],"target":[31],"data,":[32],"defining":[33],"ontologies":[34],"that":[35],"state":[36],"types":[38],"entities":[40,48,102],"on":[41,113,118,142,152],"certain":[43],"field":[44],"how":[46],"these":[47,72],"are":[49,74,111,145,159],"interrelated.":[50],"work,":[53],"we":[54,86],"introduce":[55],"OntoRXN,":[56],"novel":[58],"ontology":[59,116,144],"describing":[60],"reaction":[62,93],"networks":[63,73],"constructed":[64],"from":[65],"computational":[66,106],"chemistry":[67],"calculations.":[68,107],"Under":[69],"our":[70],"paradigm,":[71],"handled":[75],"as":[76],"undirected":[77],"graphs,":[78],"without":[79],"assuming":[80],"any":[81],"traversal":[82],"direction.":[83],"From":[84],"there,":[85],"core":[89],"class":[90],"including":[92],"steps,":[94],"network":[95],"stages,":[96],"chemical":[97,149],"species,":[98],"lower-level":[101],"individual":[105,109],"These":[108],"calculations":[110],"founded":[112],"OntoCompChem":[115],"ioChem-BD":[120],"database,":[121],"where":[122],"information":[123],"is":[124,132],"parsed":[125],"stored":[127],"CML":[129],"format.":[130],"OntoRXN":[131],"introduced":[133],"through":[134,161],"several":[135],"examples":[136],"which":[138],"knowledge":[139,157],"graphs":[140,158],"based":[141],"generated":[146],"different":[148],"systems":[150],"available":[151],"ioChem-BD.":[153],"Finally,":[154],"resulting":[156],"explored":[160],"SPARQL":[162],"queries,":[163],"illustrating":[164],"power":[166],"approach":[170],"to":[171,179],"standardize":[172],"analysis":[174],"intricate":[176],"datasets":[177],"simplify":[180],"development":[182],"complex":[184],"workflows.":[185]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
