Import literature

[cybersiddhu]

Export of non pubmed entries from multigenome database is broken.

$_> modware-export dictynonpub2bib [--options] -o dictygenomesnonpub.bib

Since its only even less than handful probably it is better to leave them from exporting and just manually import them later on.

[cybersiddhu]

Importing is done from bibtex file.

Bibtex format of a pubmed entry

@article{pmid20070309,
journal = {{Cell. Microbiol.}}
title = {{Loss of Dictyostelium ATG9 results in a pleiotropic phenotype affecting growth, development, phagocytosis and clearance and replication of Legionella pneumophila.}}
status = {ppublish}
nlmuniqueid = {100883691}
pmid = {20070309}
year = {2010}
volume = {12}
pages = {765-80}
doi = {10.1111/j.1462-5822.2010.01432.x}
month = {jun}
issn = {1462-5822}
abstract = {Infection of Dictyostelium discoideum with Legionella pneumophila resulted in a large number of differentially regulated genes among them three core autophagy genes, ATG8, ATG9 and ATG16. Macroautophagy contributes to many physiological and pathological processes and might also constitute an important mechanism in cell-autonomous immunity. For further studies we selected the highly conserved ATG9. In colocalization studies with GFP-tagged ATG9 and different organelle marker proteins we neither observed colocalization with mitochondria, the ER nor lysosomes. However, there was partial colocalization with the Golgi apparatus and many ATG9-GFP-containing vesicles localized along microtubules and accumulated around the microtubule organizing centre. ATG9-deficient cells had pleiotropic defects. In addition to growth defects they displayed severe developmental defects, consistent with the known role of autophagy in Dictyostelium development. Unexpectedly, the ATG9 mutant also had a strong phagocytosis defect that was particularly apparent when infecting the cells with L. pneumophila. However, those Legionellae that entered the host could multiply better in mutant than in wild-type cells, because of a less efficient clearance in the early and a more efficient replication in the late phase of infection. We conclude that ATG9 and hence macroautophagy has a protective role during pathogen infection.}
author = {Tung, Sze Man SM and Unal, Can C and Ley, Alexandra A and Peña, Cohue C and Tunggal, Budi B and Noegel, Angelika A AA and Krut, Oleg O and Steinert, Michael M and Eichinger, Ludwig L }
timestamp = {2010.01.18}
}

Bibtex format of a non-pubmed entry

@article{endnotePUB6686,
id = {PUB6686}
journal = {{Euk. Cell}}
title = {{CulB, a putative ubiquitin ligase subunit, regulates prestalk cell differentiation and morphogenesis in Dictyostelium spp.}}
volume = {1}
year = {2002}
pages = {126-136}
author = {{Wang, B. and Kuspa, A.}}
timestamp = {2003.01.13}
}

[cybersiddhu]

Mapping of bibtex to chado schema

Mapping will be describe as table.column format.

• @article: The type, map to pub.type_id --> cvterm.name -> cv.name. It should use pub_type cv namespace. For one with pubmed id cvterm.name is journal article and for others it is unpublished.
• pmid20070309: citation key. There will be two values here, source and unique id. pmid is the source here and maps to pub.pubplace
• journal: pub.series_name
• title: pub.title
• volume: pub.volume
• year: pub.pyear
• pages: pub.pages. The page value goes as it is, no separation of start and end page.
• status: pubprop.value -> cvterm.name(status) -> cv(pub_type)
• pmid: pub.uniquename. This is pubmed id and for this the pub.pubplace should always be pubmed.
• doi: pubprop.value -> cvterm.name(doi) -> cv(pub_type)
• month: pubprop.value -> cvterm.name(month) -> cv(pub_type)
• issn: pubprop.value -> cvterm.name(issn) -> cv(pub_type)
• abstract: pubprop.value -> cvterm.name(abstract) -> cv(pub_type)
• author: pubauthor.surname for anything before the comma,. The rest of it goes to pubauthor.givennames. pubauthor.rank to represent first, second, third author etc.

[cybersiddhu]

Features to remember

• Every pubmed record is refreshed, any stale information will be removed.
• Includes DOI in this import.
• DOI will not retire, so at least the full text links will always be live.

[cybersiddhu]

Questions

• Could all non-pubmed entries have DOI ?
• Is it possible to have DOI for GO_REFs ?

[cybersiddhu]

Download pub_type ontology from here ftp://ftp.flybase.org/releases/current/precomputed_files/ontologies/flybase_controlled_vocabulary.obo.zip.