kevinschaper
commented
3 years ago Specific types for the type slot could potentially be derived from MOD specific strings in MODReferenceTypes[].referenceType, but I unless I hear otherwise I'm going to assume that our use case doesn't require a level of detail granular enough to be worth mapping all of these terms:
292454 "Peer Reviewed Article" 135421 "JOURNAL ARTICLE" 110034 "paper" 40243 "DNA/RNA sequence record" 37643 "abstract" 36316 "Journal" 25847 "Journal_article" 23060 "Meeting_abstract" 14984 "review" 9249 "thesis" 7647 "Review" 7160 "personal communication to FlyBase" 3157 "Thesis" 3072 "Gazette_article" 2974 "stock list" 2730 "protein sequence record" 2248 "MGI Curation Record" 2136 "note" 1983 "Journal Article" 1702 "MGI Direct Data Submission" 1522 "Newsletter" 1089 "Other" 921 "Chapter" 859 "book" 732 "Research Support, Non-U.S. Gov't" 657 "supplementary material" 631 "Comment" 595 "erratum" 554 "Book" 481 "Abstract" 409 "letter" 401 "Book_chapter" 396 "patent" 320 "conference report" 308 "Research Support, N.I.H., Extramural" 299 "Conference Proceedings/Abstracts" 276 "Micropublication" 249 "FlyBase analysis" 216 "Unreviewed Article" 208 "film" 206 "unpublished" 191 "book review" 176 "News" 173 "Personal Communication" 168 "news article" 162 "Published_erratum" 150 "PERSONAL COMMUNICATION" 149 "obituary" 146 "teaching note" 138 "Letter" 129 "WormBook" 126 "biography" 121 "Method" 105 "editorial" 102 "bibliographic list" 100 "DIRECT DATA TRANSFER" 98 "Curation" 86 "Research Support, U.S. Gov't, Non-P.H.S." 85 "Editorial" 80 "poster" 76 "Unknown" 75 "BOOK REVIEW" 71 "curated genome annotation" 70 "MGI Data Load" 60 "interview" 49 "Historical_article" 46 "website" 41 "Unpublished" 37 "Interview" 36 "WEBSITE" 34 "Active Curation" 31 "retraction" 30 "Annual Report/Bulletin" 27 "Biography" 25 "Congresses" 22 "autobiography" 19 "External Resource" 17 "Research Support, N.I.H., Intramural" 16 "Comparative Study" 15 "UNKNOWN" 15 "Dissertation/Thesis" 14 "Retraction_of_publication" 13 "press release" 13 "Retracted_publication" 13 "Published Erratum" 13 "Movie" 10 "JAX Notes" 9 "Evaluation Study" 8 "spoof" 8 "species list" 7 "poem" 6 "white paper" 6 "database" 6 "Historical Article" 6 "ABSTRACT" 5 "Video-Audio Media" 5 "Validation Study" 5 "Lectures" 4 "Introductory Journal Article" 3 "preprint" 3 "Interactive_tutorial" 2 "Technical_report" 2 "Research Support, U.S. Gov't, P.H.S." 2 "Case Reports" 1 "lecture" 1 "Retracted Publication" 1 "Personal Narrative" 1 "Not Specified" 1 "Monograph" 1 "Meta-Analysis" 1 "Dataset" 1 "BOOK" 1 "Autobiography"
The Alliance has a well defined literature ingest format that aligns publications from MOD members. Comparing with fields available in the ZFIN publication download, for example, this is a much richer ingest format.
For the publication type, there is an "allianceCategory" field that is an enum that is a nice higher level field that is aligned across MODs that should help for distinguishing which (even higher level) biolink class each publication is.