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Bio2RDF v5 release preparation#462

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micheldumontier merged 79 commits intorelease3bio2rdf/bio2rdf-scripts:release3from

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Jun 30, 2020

Commits

Commits on Mar 19, 2013

• Added MIT license hopefully as per mailing list discussion.

  

  Jeremy Carroll

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Commits on Jun 16, 2013

• Merge remote-tracking branch 'bio2rdf-master/master'

  micheldumontier

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Commits on Aug 8, 2013

• Merge pull request #194 from jeremycarroll/with-license

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  micheldumontier

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• Update README.md

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  micheldumontier

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Commits on Sep 17, 2013

• Fixed (line 392): removed premature closing parenthesis in chembl quad instantiation ~Paul Rigor

  theoryno3

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• Merge pull request #320 from theoryno3/patch-1

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  micheldumontier

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Commits on Jan 24, 2014

• added license notice at the bottom

  jctoledo

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• Update README.md

  jctoledo

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• Update README.md

  jctoledo

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• Update MIT-LICENSE.txt

  jctoledo

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• Update README.md

  jctoledo

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Commits on Feb 2, 2016

• merged release3

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  zorino

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• Merge pull request #428 from zorino/master

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  micheldumontier

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• Merge branch 'master' of https://github.com/bio2rdf/bio2rdf-scripts

  micheldumontier

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Commits on Mar 27, 2016

• changed gene id to uppercase organism id #430

  micheldumontier

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• include more than just human genes

  micheldumontier

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• fixed field tokenizer #429

  micheldumontier

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Commits on Mar 29, 2016

• fixed multi entry parsing error #432

  micheldumontier

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• parse the mesh ids out of the xml files #433

  micheldumontier

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• use Bio2RDF's GO to replace labels with codes #431

  micheldumontier

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Commits on Apr 1, 2016

• fixed changed column issue #436

  micheldumontier

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• fixed parsing of multi-value fields for pharmgkb gene data #436

  micheldumontier

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• added parselist to drugs. more ids extracted #437

  micheldumontier

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• Fixed disease data parsing #438

  micheldumontier

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• fixed pharmgkb gene labels #436

  micheldumontier

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• generating only a single entity-entity-association #439

  micheldumontier

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Commits on Apr 11, 2016

• Fixed clinical and variant annotations parsing #441

  micheldumontier

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• Fixed phargmbk pathway download #442

  micheldumontier

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• complete pharmgkb pathway parse #442

  micheldumontier

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Commits on Apr 12, 2016

• fix for multiple control and cell types #442

  micheldumontier

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• added 'map' to kegg pathway identifiers, to conform with source #440

  micheldumontier

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Commits on May 13, 2016

• Update README.md

  micheldumontier

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Commits on May 19, 2016

• fixed premature end of parse due to blank entry

  micheldumontier

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Commits on Jul 22, 2016

• simplify column id and includes a column fix for aliases

  micheldumontier

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Commits on Jul 25, 2016

• Merge pull request #444 from micheldumontier/master

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  micheldumontier

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Commits on Nov 1, 2016

• MD5 Hash Drugbank Mixture URIs

  maulikkamdar

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Commits on Jan 23, 2017

• Merge pull request #448 from bio2rdf/release3

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  Yifan Ning

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• Merge pull request #449 from bio2rdf/release3

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  Yifan Ning

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Commits on Jan 30, 2017

• Merge pull request #450 from bio2rdf/release3

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  Yifan Ning

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• Merge pull request #451 from bio2rdf/release3

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  Yifan Ning

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Commits on Apr 14, 2017

• Array_shift only pops the first location from the stack, therefore randomly selecting a location where the trial was executed. Converted into a loop which parses all locations

  

  Johan van Soest

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Commits on Aug 30, 2017

• adding arc2 through composer

  micheldumontier

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Commits on Jan 23, 2018

• added check for null oversight value

  micheldumontier

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Commits on Mar 27, 2018

• Link DOIs to preferred resolver

  katrinleinweber

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• Merge pull request #456 from katrinleinweber/resolve-DOIs-securely

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  micheldumontier

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Commits on Oct 29, 2018

• fixed merge error

  micheldumontier

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Commits on Feb 11, 2020

• Use HTTPS instead of HTTP to resolve dependencies

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  JLLeitschuh

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Commits on May 25, 2020

• update path

  micheldumontier

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• updated with new format

  micheldumontier

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Commits on May 26, 2020

• updates to file processing; removed automatic download

  micheldumontier

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• update the orphanet disease processor

  micheldumontier

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• escape the definition

  micheldumontier

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  e26d8d5

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• fixes for orphanet genes

  micheldumontier

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• correctly parse the list of external references for the genes

  micheldumontier

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• added source of validation to gene disease association

  micheldumontier

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• revised processing of orphanet signs and frequencies

  micheldumontier

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Commits on May 27, 2020

• id fixes; addition of prevalence parser

  micheldumontier

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Commits on May 31, 2020

• fix for weird character exceptions and multiple entries

  micheldumontier

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Commits on Jun 1, 2020

• added check for entries without abstract

  micheldumontier

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• changed output file names

  micheldumontier

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• removed html tags, extra spaces, and escaped special chars in abstract

  micheldumontier

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• update the path and version number of the latest entry

  micheldumontier

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• added domain namespaces; new url for goa; changed output file format

  micheldumontier

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• made it so you can create the bioportal download directory for apo.obo

  micheldumontier

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• replaced empty string initialisation to array

  micheldumontier

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• fixed string initialisation of array

  micheldumontier

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• removed files no longer available; changed output file names

  micheldumontier

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• escape allele label

  micheldumontier

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• downloads zip file with all entries; fixes xml string processing problems

  micheldumontier

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  c16a16a

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• updated download file location

  micheldumontier

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  748a480

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• updates for mgi inc. download location, column mappings, and identifiers

  micheldumontier

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  416c212

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• fixed comparator error

  micheldumontier

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  1fc4163

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• updates to wormbase

  micheldumontier

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Commits on Jun 2, 2020

• fixes for taxonomy

  micheldumontier

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  75e0743

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• changes to download urls; fixes to record processor

  micheldumontier

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Commits on Jun 9, 2020

• Merge pull request #460 from bio2rdf/release3

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  micheldumontier

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• fix for namespace not provided in obo file

  micheldumontier

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Commits on Jun 30, 2020

• Merge pull request #459 from JLLeitschuh/fix/JLL/use_https_to_resolve_dependencies

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  micheldumontier

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• Merge pull request #454 from jvsoest/include_all_locations

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  micheldumontier

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