{"id":"https://openalex.org/W2006026068","doi":"https://doi.org/10.1186/1758-2946-4-15","title":"The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem","display_name":"The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem","publication_year":2012,"publication_date":"2012-08-07","ids":{"openalex":"https://openalex.org/W2006026068","doi":"https://doi.org/10.1186/1758-2946-4-15","mag":"2006026068","pmid":"https://pubmed.ncbi.nlm.nih.gov/22870956"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-4-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-4-15","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-4-15","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/10.1186/1758-2946-4-15","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037593158","display_name":"Weerapong Phadungsukanan","orcid":null},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Weerapong Phadungsukanan","raw_affiliation_strings":["Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK. mk306@cam.ac.uk","Department of Chemical Engineering and Biotechnology, New Museums Site, University of Cambridge, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK. mk306@cam.ac.uk","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Chemical Engineering and Biotechnology, New Museums Site, University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062571604","display_name":"Markus Kraft","orcid":"https://orcid.org/0000-0002-4293-8924"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Markus Kraft","raw_affiliation_strings":["Department of Chemical Engineering and Biotechnology, New Museums Site, University of Cambridge, Pembroke Street, Cambridge, CB2 3RA, UK","Department of Chemical Engineering and Biotechnology, New Museums Site, University of Cambridge, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering and Biotechnology, New Museums Site, University of Cambridge, Pembroke Street, Cambridge, CB2 3RA, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Chemical Engineering and Biotechnology, New Museums Site, University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029919865","display_name":"Joe Townsend","orcid":"https://orcid.org/0000-0002-5478-0028"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Joe A Townsend","raw_affiliation_strings":["Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK","Department of Chemistry; University of Cambridge; Cambridge; UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Chemistry; University of Cambridge; Cambridge; UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041092827","display_name":"Peter Murray\u2010Rust","orcid":"https://orcid.org/0000-0003-3386-3972"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter Murray-Rust","raw_affiliation_strings":["Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK","Department of Chemistry; University of Cambridge; Cambridge; UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Chemistry; University of Cambridge; Cambridge; UK","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5037593158"],"corresponding_institution_ids":["https://openalex.org/I241749"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":3.0942,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.91563253,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"4","issue":"1","first_page":"15","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9889000058174133,"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"}},"topics":[{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9889000058174133,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9836999773979187,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9821000099182129,"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/markup-language","display_name":"Markup language","score":0.7306069731712341},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.729502260684967},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.5383184552192688},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.496772825717926},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.39743632078170776},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3567339777946472},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35039079189300537},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.22005081176757812}],"concepts":[{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.7306069731712341},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.729502260684967},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.5383184552192688},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.496772825717926},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.39743632078170776},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3567339777946472},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35039079189300537},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.22005081176757812}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1758-2946-4-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-4-15","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-4-15","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:22870956","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22870956","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:772cc53cf8db4f21b8cc93d5abee69b0","is_oa":false,"landing_page_url":"https://doaj.org/article/772cc53cf8db4f21b8cc93d5abee69b0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"Journal of Cheminformatics, Vol 4, Iss 1, p 15 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2438773","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3434037","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/243673","is_oa":true,"landing_page_url":"http://www.dspace.cam.ac.uk/handle/1810/243673","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-4-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-4-15","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-4-15","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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6499999761581421}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2006026068.pdf","grobid_xml":"https://content.openalex.org/works/W2006026068.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W13024833","https://openalex.org/W1600191139","https://openalex.org/W1744779065","https://openalex.org/W1965014786","https://openalex.org/W1973364310","https://openalex.org/W1973825737","https://openalex.org/W2010918631","https://openalex.org/W2022950330","https://openalex.org/W2025138246","https://openalex.org/W2034504949","https://openalex.org/W2037993052","https://openalex.org/W2047600440","https://openalex.org/W2053778958","https://openalex.org/W2058673890","https://openalex.org/W2064270057","https://openalex.org/W2077387189","https://openalex.org/W2080623877","https://openalex.org/W2096394062","https://openalex.org/W2097433659","https://openalex.org/W2114326383","https://openalex.org/W2141447924","https://openalex.org/W2153580566","https://openalex.org/W2160845726","https://openalex.org/W2166490655","https://openalex.org/W2169678694","https://openalex.org/W2242459625","https://openalex.org/W2328512042","https://openalex.org/W2780912412"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4385386698","https://openalex.org/W4388119604","https://openalex.org/W2954418080","https://openalex.org/W3121570353","https://openalex.org/W818235636","https://openalex.org/W4388119676","https://openalex.org/W1566913699","https://openalex.org/W2081328318","https://openalex.org/W2788308474"],"abstract_inverted_index":{":":[0],"This":[1],"paper":[2,77],"introduces":[3],"a":[4,45],"subdomain":[5],"chemistry":[6,11,34,52,105],"format":[7,43],"for":[8,63],"storing":[9],"computational":[10,33,104],"data":[12],"called":[13],"CompChem.":[14],"It":[15],"has":[16],"been":[17],"developed":[18],"based":[19],"on":[20,36],"the":[21,39,80,97],"design,":[22],"concepts":[23],"and":[24,72,90,99],"methodologies":[25],"of":[26,38,48,54,96,111],"Chemical":[27],"Markup":[28],"Language":[29],"(CML)":[30],"by":[31,115],"adding":[32],"semantics":[35],"top":[37],"CML":[40],"Schema.":[41],"The":[42,76,109],"allows":[44],"wide":[46],"range":[47],"ab":[49],"initio":[50],"quantum":[51],"calculations":[53,61],"individual":[55],"molecules":[56],"to":[57],"be":[58],"stored.":[59],"These":[60],"include,":[62],"example,":[64],"single":[65],"point":[66],"energy":[67],"calculation,":[68],"molecular":[69],"geometry":[70],"optimization,":[71],"vibrational":[73],"frequency":[74],"analysis.":[75],"also":[78],"describes":[79],"supporting":[81],"infrastructure,":[82],"such":[83],"as":[84],"processing":[85],"software,":[86],"dictionaries,":[87],"validation":[88],"tools":[89],"database":[91],"repositories.":[92],"In":[93],"addition,":[94],"some":[95],"challenges":[98],"difficulties":[100],"in":[101],"developing":[102],"common":[103],"dictionaries":[106],"are":[107,113],"discussed.":[108],"uses":[110],"CompChem":[112],"illustrated":[114],"two":[116],"practical":[117],"applications.":[118]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
