{"id":"https://openalex.org/W2144687011","doi":"https://doi.org/10.1186/1471-2105-9-28","title":"The XBabelPhish MAGE-ML and XML Translator","display_name":"The XBabelPhish MAGE-ML and XML Translator","publication_year":2008,"publication_date":"2008-01-18","ids":{"openalex":"https://openalex.org/W2144687011","doi":"https://doi.org/10.1186/1471-2105-9-28","mag":"2144687011","pmid":"https://pubmed.ncbi.nlm.nih.gov/18205924"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-28","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-28","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-28","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-28","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101932607","display_name":"Dieter Maier","orcid":"https://orcid.org/0000-0003-1208-2093"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Don Maier","raw_affiliation_strings":["Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA. dMaier@genome.stanford.edu","Department of Biochemistry Stanford University School of Medicine, \u00a0, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA. dMaier@genome.stanford.edu","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Biochemistry Stanford University School of Medicine, \u00a0, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076703213","display_name":"Farrell Wymore","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Farrell Wymore","raw_affiliation_strings":["Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA","Department of Biochemistry Stanford University School of Medicine, \u00a0, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Biochemistry Stanford University School of Medicine, \u00a0, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058333700","display_name":"Gavin Sherlock","orcid":"https://orcid.org/0000-0002-1692-4983"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gavin Sherlock","raw_affiliation_strings":["Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA","Dept. of Genetics, Stanford University, School of Medicine, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Dept. of Genetics, Stanford University, School of Medicine, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113321696","display_name":"Catherine A. Ball","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Catherine A Ball","raw_affiliation_strings":["Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA","Department of Biochemistry Stanford University School of Medicine, \u00a0, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Biochemistry Stanford University School of Medicine, \u00a0, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101932607"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4136,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.64782473,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"9","issue":"1","first_page":"28","last_page":"28"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9998000264167786,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9998000264167786,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9957000017166138,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9937999844551086,"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/computer-science","display_name":"Computer science","score":0.8508443236351013},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.7051380276679993},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.548115611076355},{"id":"https://openalex.org/keywords/document-structure-description","display_name":"Document Structure Description","score":0.5279406905174255},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5207952857017517},{"id":"https://openalex.org/keywords/xml-schema","display_name":"XML Schema (W3C)","score":0.5058002471923828},{"id":"https://openalex.org/keywords/xquery","display_name":"XQuery","score":0.48676204681396484},{"id":"https://openalex.org/keywords/xml-framework","display_name":"XML framework","score":0.472357839345932},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4670606553554535},{"id":"https://openalex.org/keywords/efficient-xml-interchange","display_name":"Efficient XML Interchange","score":0.45864301919937134},{"id":"https://openalex.org/keywords/xml-validation","display_name":"XML validation","score":0.4332715570926666},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.40682172775268555},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33292096853256226},{"id":"https://openalex.org/keywords/document-type-definition","display_name":"Document type definition","score":0.30649644136428833},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.27988559007644653}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8508443236351013},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.7051380276679993},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.548115611076355},{"id":"https://openalex.org/C68699486","wikidata":"https://www.wikidata.org/wiki/Q265904","display_name":"Document Structure Description","level":3,"score":0.5279406905174255},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5207952857017517},{"id":"https://openalex.org/C40713593","wikidata":"https://www.wikidata.org/wiki/Q16342","display_name":"XML Schema (W3C)","level":5,"score":0.5058002471923828},{"id":"https://openalex.org/C2780512708","wikidata":"https://www.wikidata.org/wiki/Q850661","display_name":"XQuery","level":4,"score":0.48676204681396484},{"id":"https://openalex.org/C21761406","wikidata":"https://www.wikidata.org/wiki/Q8042330","display_name":"XML framework","level":3,"score":0.472357839345932},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4670606553554535},{"id":"https://openalex.org/C11508877","wikidata":"https://www.wikidata.org/wiki/Q1124477","display_name":"Efficient XML Interchange","level":3,"score":0.45864301919937134},{"id":"https://openalex.org/C55348073","wikidata":"https://www.wikidata.org/wiki/Q595926","display_name":"XML validation","level":3,"score":0.4332715570926666},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.40682172775268555},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33292096853256226},{"id":"https://openalex.org/C84314905","wikidata":"https://www.wikidata.org/wiki/Q212327","display_name":"Document type definition","level":4,"score":0.30649644136428833},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.27988559007644653}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014941","descriptor_name":"Work Simplification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014941","descriptor_name":"Work Simplification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014941","descriptor_name":"Work Simplification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-28","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-28","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-28","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18205924","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18205924","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d1b791b66fdf4252b47e089afd0c0e87","is_oa":true,"landing_page_url":"https://doaj.org/article/d1b791b66fdf4252b47e089afd0c0e87","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 28 (2008)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1832688","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2233607","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-28","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-28","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-28","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4300000071525574}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144687011.pdf","grobid_xml":"https://content.openalex.org/works/W2144687011.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W13024833","https://openalex.org/W172857819","https://openalex.org/W1486283310","https://openalex.org/W1504548550","https://openalex.org/W1573136363","https://openalex.org/W1985098050","https://openalex.org/W2134532199","https://openalex.org/W2143129697","https://openalex.org/W2240553986","https://openalex.org/W2798365443","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2141581404","https://openalex.org/W1496558728","https://openalex.org/W2612836072","https://openalex.org/W1568675419","https://openalex.org/W1997200271","https://openalex.org/W2888238649","https://openalex.org/W1551963477","https://openalex.org/W2591751462","https://openalex.org/W4206399782","https://openalex.org/W2752365879"],"abstract_inverted_index":{"XBabelPhish":[0],"provides":[1],"a":[2],"way":[3],"to":[4,21],"inter-translate":[5],"MAGE-ML":[6],"variants":[7],"for":[8],"improved":[9],"interchange":[10],"of":[11,34],"microarray":[12],"experiment":[13],"information.":[14],"More":[15],"generally,":[16],"it":[17],"can":[18],"be":[19],"used":[20],"transform":[22],"most":[23,35],"XML":[24,36],"files,":[25],"including":[26],"very":[27],"large":[28],"ones":[29],"that":[30],"exceed":[31],"the":[32],"capacity":[33],"tools.":[37]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}