{"id":"https://openalex.org/W4393906038","doi":"https://doi.org/10.1093/bioinformatics/btae174","title":"The IDSM mass spectrometry extension: searching mass spectra using SPARQL","display_name":"The IDSM mass spectrometry extension: searching mass spectra using SPARQL","publication_year":2024,"publication_date":"2024-03-29","ids":{"openalex":"https://openalex.org/W4393906038","doi":"https://doi.org/10.1093/bioinformatics/btae174","pmid":"https://pubmed.ncbi.nlm.nih.gov/38561173"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae174","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae174","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae174/57136570/btae174.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae174/57136570/btae174.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079524677","display_name":"Jakub Galgonek","orcid":"https://orcid.org/0000-0002-7038-544X"},"institutions":[{"id":"https://openalex.org/I4210145889","display_name":"Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry","ror":"https://ror.org/04nfjn472","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210145889"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Jakub Galgonek","raw_affiliation_strings":["Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo n\u00e1m\u011bst\u00ed 2 , Prague 160 00, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo n\u00e1m\u011bst\u00ed 2 , Prague 160 00, Czech Republic","institution_ids":["https://openalex.org/I4210145889"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031688867","display_name":"Ji\u0159\u0131\u0301 Vondr\u00e1\u0161ek","orcid":"https://orcid.org/0000-0002-6066-973X"},"institutions":[{"id":"https://openalex.org/I4210145889","display_name":"Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry","ror":"https://ror.org/04nfjn472","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210145889"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ji\u0159\u00ed Vondr\u00e1\u0161ek","raw_affiliation_strings":["Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo n\u00e1m\u011bst\u00ed 2 , Prague 160 00, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo n\u00e1m\u011bst\u00ed 2 , Prague 160 00, Czech Republic","institution_ids":["https://openalex.org/I4210145889"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079524677"],"corresponding_institution_ids":["https://openalex.org/I4210145889"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4579,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.61932781,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"40","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9986000061035156,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9986000061035156,"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sparql","display_name":"SPARQL","score":0.7797790765762329},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7540698051452637},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.6721877455711365},{"id":"https://openalex.org/keywords/mass-spectrum","display_name":"Mass spectrum","score":0.602226734161377},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5355643630027771},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.49265843629837036},{"id":"https://openalex.org/keywords/elixir","display_name":"Elixir (programming language)","score":0.4925904870033264},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4893900752067566},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.45998305082321167},{"id":"https://openalex.org/keywords/data-source","display_name":"Data source","score":0.426106333732605},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.42185741662979126},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.3949222266674042},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.30187249183654785},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.22859883308410645},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2119886577129364},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.16024768352508545},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13920509815216064},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.09448692202568054}],"concepts":[{"id":"https://openalex.org/C41009113","wikidata":"https://www.wikidata.org/wiki/Q54871","display_name":"SPARQL","level":4,"score":0.7797790765762329},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7540698051452637},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.6721877455711365},{"id":"https://openalex.org/C40325409","wikidata":"https://www.wikidata.org/wiki/Q2360668","display_name":"Mass spectrum","level":3,"score":0.602226734161377},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5355643630027771},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49265843629837036},{"id":"https://openalex.org/C103472402","wikidata":"https://www.wikidata.org/wiki/Q5362035","display_name":"Elixir (programming language)","level":2,"score":0.4925904870033264},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4893900752067566},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.45998305082321167},{"id":"https://openalex.org/C2983685735","wikidata":"https://www.wikidata.org/wiki/Q5227355","display_name":"Data source","level":2,"score":0.426106333732605},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.42185741662979126},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.3949222266674042},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.30187249183654785},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.22859883308410645},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2119886577129364},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.16024768352508545},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13920509815216064},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.09448692202568054},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae174","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae174","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae174/57136570/btae174.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38561173","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38561173","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11034985","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11034985","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11034985/pdf/btae174.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae174","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae174","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae174/57136570/btae174.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1143656335","display_name":null,"funder_award_id":"101082304","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G363053650","display_name":"Iwasawa theory of p-adic Lie extensions","funder_award_id":"202305","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7343488542","display_name":null,"funder_award_id":"101082304","funder_id":"https://openalex.org/F4320334322","funder_display_name":"HORIZON EUROPE Framework Programme"},{"id":"https://openalex.org/G8051717526","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320311039","display_name":"Ministry of Higher Education and Scientific Research","ror":"https://ror.org/00kab6t91"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334322","display_name":"HORIZON EUROPE Framework Programme","ror":null},{"id":"https://openalex.org/F4320334679","display_name":"Research Executive Agency","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4393906038.pdf"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1508604947","https://openalex.org/W1852306145","https://openalex.org/W1935434993","https://openalex.org/W2049625541","https://openalex.org/W2110017950","https://openalex.org/W2110279208","https://openalex.org/W2123152121","https://openalex.org/W2144427809","https://openalex.org/W2146736600","https://openalex.org/W2155478691","https://openalex.org/W2163917093","https://openalex.org/W2257876130","https://openalex.org/W2259172389","https://openalex.org/W2531883117","https://openalex.org/W2548357532","https://openalex.org/W2792232697","https://openalex.org/W2807294144","https://openalex.org/W2955385017","https://openalex.org/W2957016348","https://openalex.org/W2965518110","https://openalex.org/W3081878206","https://openalex.org/W3160452578","https://openalex.org/W3170771812","https://openalex.org/W3211718555","https://openalex.org/W4281658583","https://openalex.org/W4310948626","https://openalex.org/W4387935536","https://openalex.org/W4393547491","https://openalex.org/W6692126448"],"related_works":["https://openalex.org/W3160690796","https://openalex.org/W2945781956","https://openalex.org/W2038821533","https://openalex.org/W2295889387","https://openalex.org/W2966875286","https://openalex.org/W76044956","https://openalex.org/W129667569","https://openalex.org/W3142934089","https://openalex.org/W2900692317","https://openalex.org/W2528665947"],"abstract_inverted_index":{"The":[0,13,22],"extension":[1],"is":[2,9],"an":[3],"integral":[4],"part":[5],"of":[6,25],"IDSM,":[7],"which":[8],"available":[10,19,30],"at":[11,20,34],"https://idsm.elixir-czech.cz.":[12],"manual":[14],"and":[15],"usage":[16],"examples":[17],"are":[18,29],"https://idsm.elixir-czech.cz/docs/ms.":[21],"source":[23],"codes":[24],"all":[26],"IDSM":[27],"parts":[28],"under":[31],"open-source":[32],"licences":[33],"https://github.com/idsm-src.":[35]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
