{"id":"https://openalex.org/W2963037859","doi":"https://doi.org/10.1186/s13321-019-0349-4","title":"DNAmod: the DNA modification database","display_name":"DNAmod: the DNA modification database","publication_year":2019,"publication_date":"2019-04-23","ids":{"openalex":"https://openalex.org/W2963037859","doi":"https://doi.org/10.1186/s13321-019-0349-4","mag":"2963037859","pmid":"https://pubmed.ncbi.nlm.nih.gov/31016417","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/6478773"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0349-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0349-4","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/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0349-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044134961","display_name":"Ankur Jai Sood","orcid":"https://orcid.org/0000-0002-3345-7934"},"institutions":[{"id":"https://openalex.org/I2802654988","display_name":"Princess Margaret Cancer Centre","ror":"https://ror.org/03zayce58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ankur Jai Sood","raw_affiliation_strings":["Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower 15-701, 101 College Street, Toronto, ON, M5G 1L7, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower 15-701, 101 College Street, Toronto, ON, M5G 1L7, Canada","institution_ids":["https://openalex.org/I2802654988","https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058663021","display_name":"Coby Viner","orcid":"https://orcid.org/0000-0001-8097-6991"},"institutions":[{"id":"https://openalex.org/I2802654988","display_name":"Princess Margaret Cancer Centre","ror":"https://ror.org/03zayce58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Coby Viner","raw_affiliation_strings":["Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower 11-311, 101 College Street, Toronto, ON, M5G 1L7, Canada"],"affiliations":[{"raw_affiliation_string":"Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower 11-311, 101 College Street, Toronto, ON, M5G 1L7, Canada","institution_ids":["https://openalex.org/I2802654988"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043633648","display_name":"Michael M. Hoffman","orcid":"https://orcid.org/0000-0002-4517-1562"},"institutions":[{"id":"https://openalex.org/I2802654988","display_name":"Princess Margaret Cancer Centre","ror":"https://ror.org/03zayce58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Michael M. Hoffman","raw_affiliation_strings":["Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower 15-701, 101 College Street, Toronto, ON, M5G 1L7, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower 15-701, 101 College Street, Toronto, ON, M5G 1L7, Canada","institution_ids":["https://openalex.org/I2802654988","https://openalex.org/I185261750"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582,"provenance":"doaj"},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582,"provenance":"doaj"},"fwci":3.554,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":67,"citation_normalized_percentile":{"value":0.999983,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"11","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA Methylation and Modification in Gene Expression","score":0.9996,"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/T11482","display_name":"RNA Methylation and Modification in Gene Expression","score":0.9996,"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/T10269","display_name":"Epigenetic Modifications and Their Functional Implications","score":0.999,"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/T13157","display_name":"Protein Arginine Methylation in Mammals","score":0.9829,"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/mrna-modification","display_name":"mRNA modification","score":0.557325},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA Methylation","score":0.514399}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.589565},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.49821782},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4511605},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.42124024},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24287197},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19785446}],"mesh":[],"locations_count":5,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0349-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0349-4","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/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://europepmc.org/articles/pmc6478773","pdf_url":"https://europepmc.org/articles/pmc6478773?pdf=render","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":true,"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":["European Bioinformatics Institute"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478773","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://doi.org/10.1101/071712","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2016/08/26/071712.full.pdf","source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31016417","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0349-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0349-4","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/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[],"grants":[{"funder":"https://openalex.org/F4320311559","funder_display_name":"Princess Margaret Cancer Foundation","award_id":"None"},{"funder":"https://openalex.org/F4320313290","funder_display_name":"Ontario Institute for Cancer Research","award_id":"CSC-FR-UHN"},{"funder":"https://openalex.org/F4320320118","funder_display_name":"Canadian Cancer Society","award_id":"703827"},{"funder":"https://openalex.org/F4320321886","funder_display_name":"Ontario Ministry of Research, Innovation and Science","award_id":"ER-15-11-223"},{"funder":"https://openalex.org/F4320322015","funder_display_name":"University of Toronto","award_id":null},{"funder":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research","award_id":"201512MSH-360970"},{"funder":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada","award_id":"CGSM-2015"}],"datasets":[],"versions":[],"referenced_works_count":53,"referenced_works":["https://openalex.org/W1503311137","https://openalex.org/W1508604947","https://openalex.org/W179451878","https://openalex.org/W1802567635","https://openalex.org/W1852306145","https://openalex.org/W1935434993","https://openalex.org/W1975147762","https://openalex.org/W1984066495","https://openalex.org/W2000225203","https://openalex.org/W2012916279","https://openalex.org/W2021621793","https://openalex.org/W2029004484","https://openalex.org/W2032814455","https://openalex.org/W2033377040","https://openalex.org/W2036848594","https://openalex.org/W2042545888","https://openalex.org/W2047149866","https://openalex.org/W2059188171","https://openalex.org/W2063271327","https://openalex.org/W2081816416","https://openalex.org/W2090949033","https://openalex.org/W2096525273","https://openalex.org/W2103017472","https://openalex.org/W2110279208","https://openalex.org/W2110992797","https://openalex.org/W2114326383","https://openalex.org/W2114850508","https://openalex.org/W2133620956","https://openalex.org/W2133961760","https://openalex.org/W2140611297","https://openalex.org/W2144427809","https://openalex.org/W2153928007","https://openalex.org/W2159482845","https://openalex.org/W2163964975","https://openalex.org/W2164052908","https://openalex.org/W2167616678","https://openalex.org/W2169678694","https://openalex.org/W2257561185","https://openalex.org/W2292734588","https://openalex.org/W2299876992","https://openalex.org/W2409442519","https://openalex.org/W2427806340","https://openalex.org/W2473736871","https://openalex.org/W2739174192","https://openalex.org/W2762279748","https://openalex.org/W2886382167","https://openalex.org/W2906877236","https://openalex.org/W2915489297","https://openalex.org/W4243601081","https://openalex.org/W4247447075","https://openalex.org/W4251553120","https://openalex.org/W4294216483","https://openalex.org/W4390668729"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2530322880","https://openalex.org/W2390279801","https://openalex.org/W2382290278","https://openalex.org/W2376932109","https://openalex.org/W2359140296","https://openalex.org/W2358668433","https://openalex.org/W2350741829","https://openalex.org/W2001405890","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Covalent":[0],"DNA":[1,40,54,72,85,122],"modifications,":[2,48,55],"such":[3],"as":[4,25],"5-methylcytosine":[5],"(5mC),":[6],"are":[7,22],"increasingly":[8],"the":[9,71,113],"focus":[10],"of":[11,118,129,137,142,171],"numerous":[12],"research":[13],"programs.":[14],"In":[15],"eukaryotes,":[16],"both":[17],"5mC":[18],"and":[19,34,46,87,105,116,124,147,150,164],"5-hydroxymethylcytosine":[20],"(5hmC)":[21],"now":[23],"recognized":[24],"stable":[26],"epigenetic":[27,61],"marks,":[28],"with":[29],"diverse":[30],"functions.":[31],"Bacteria,":[32],"archaea,":[33],"viruses":[35],"contain":[36],"various":[37],"other":[38],"modified":[39,121,169],"nucleobases.":[41],"Numerous":[42],"databases":[43],"describe":[44],"RNA":[45],"histone":[47],"but":[49],"no":[50],"database":[51,79,111],"specifically":[52],"catalogues":[53,84],"despite":[56],"their":[57,95,143],"broad":[58],"importance":[59],"in":[60,145],"regulation.":[62],"To":[63],"address":[64],"this":[65],"need,":[66],"we":[67],"have":[68],"developed":[69],"DNAmod:":[70],"modification":[73],"database.":[74],"DNAmod":[75,97,133,153],"is":[76],"an":[77],"open-source":[78],"(":[80],"https://dnamod.hoffmanlab.org":[81],")":[82],"that":[83],"modifications":[86],"provides":[88,98,148],"a":[89,99,125],"single":[90],"source":[91],"to":[92,102,156],"learn":[93],"about":[94],"properties.":[96],"web":[100],"interface":[101],"easily":[103],"browse":[104],"search":[106],"through":[107],"these":[108],"modifications.":[109],"The":[110],"annotates":[112],"chemical":[114,131],"properties":[115],"structures":[117],"all":[119],"curated":[120],"bases,":[123],"much":[126],"larger":[127],"list":[128],"candidate":[130],"entities.":[132],"includes":[134],"manual":[135],"annotations":[136],"available":[138],"sequencing":[139],"methods,":[140],"descriptions":[141],"occurrence":[144],"nature,":[146],"existing":[149],"suggested":[151],"nomenclature.":[152],"enables":[154],"researchers":[155],"rapidly":[157],"review":[158],"previous":[159],"work,":[160],"select":[161],"mapping":[162],"techniques,":[163],"track":[165],"recent":[166],"developments":[167],"concerning":[168],"bases":[170],"interest.":[172]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2963037859","counts_by_year":[{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2024-11-21T15:54:14.146697","created_date":"2019-07-30"}
