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Change Log

14.0.0 (2020-05-21)

Full Changelog

Merged pull requests:

  • Add Siemens MRI to platform #606 (bememea)
  • Add PET and Autorad scanners to platform #605 (bememea)
  • Add cresyl violet stain as an assay #604 (bememea)
  • Updates to modelSystemName values #603 (bememea)
  • Update definition of differential expression to be more inclusive #602 (Aryllen)
  • Add elisaType to specify a specific type of ELISA assay #601 (Aryllen)

v13.0.0 (2020-05-09)

Full Changelog

Closed issues:

  • Create a new branch for schema.org json-ld based annotations #590

Merged pull requests:

v12.2.0 (2020-03-04)

Full Changelog

Merged pull requests:

v12.1.0 (2020-02-04)

Full Changelog

Closed issues:

  • Allow alternate capitalizations of boolean values #535

Merged pull requests:

v12.0.0 (2019-11-25)

Full Changelog

Implemented enhancements:

  • Add annotations for reference genome build/assembly #120

Fixed bugs:

  • immunohistochemistry and brightfieldMicroscopy seem to be overlapping assays #419

Closed issues:

  • Add metadataType: manifest #539
  • Do we really need to control values for grant? #519
  • assay = mRNA counts #516
  • values for sex #512
  • Protocols #511
  • single cell annotations #510
  • broken links - libraryPreparationMethod #508
  • Mouse model annotation #497
  • Add metadataType key #470
  • Add more detail on release process #447
  • Need to find solution to cancer subtype #366
  • Get serious about tool/model annotations #364
  • Think more and come to some conclusion about JSON Schema and JSON-LD #351
  • Discussion about mouse behavioral analysis annotations #341
  • Recommended annotations for QC files #292
  • What are recommended sources for grants #236
  • SOP for annotating cell lines by individualId and sampleId #233
  • Clarify descriptions/source for 'platform' values to include other species #224
  • library prep platform #178

Merged pull requests:

v11.0.0 (2019-07-17)

Full Changelog

Fixed bugs:

  • Duplicate values for some keys #482

Closed issues:

  • Create a README for schema conversion #476
  • Fix camel case capitalization of annotation terms in new schemas #465
  • Migrate Milen's schema generation code to this repo #464
  • Data quality flag annotation #449
  • Update Synapse table #446

Merged pull requests:

v10.0.0 (2019-02-05)

Full Changelog

Implemented enhancements:

  • Code for automated checking of keys between minimal and project-specific files #17

Closed issues:

  • Moving drug combination data from assay to dataType #441
  • diagnosis in cell lines, animal models #432
  • Move Development section of README to CONTRIBUTING.md #391

Merged pull requests:

v9.0.0 (2018-08-21)

Full Changelog

Implemented enhancements:

Closed issues:

  • Broken link for schema definitions #397
  • Update annotations to account for JMML DHART SPORE project #394
  • Remove stale branches #390
  • need to add DESeq2 in analysis #381
  • add unit test to make sure everyone knows the annotation handshake #363
  • modelSystem #357
  • purpose of resourceType, value of some proposed terms? #350
  • Create network annotations #340
  • Additional annotation values for scRNA-Seq data #339
  • Create ability to specify type of interface for tool #338
  • add cellType: monocyte derived microglia #260
  • add cellType: iPSC-derived neurons #258
  • add cellType : iPSC derived neuronal progenitor cells #257
  • What are recommended sources for *all drug phases #235
  • Tissue homogenate vs nuclei #189

Merged pull requests:

v8.0.0 (2018-02-23)

Full Changelog

Implemented enhancements:

Merged pull requests:

v7.0.0 (2018-02-23)

Full Changelog

Implemented enhancements:

Closed issues:

  • harmonize capitilization of analysis values with source #336
  • Add link to shiny App in README.md #331
  • analysisType - ancestry #309
  • Programmatic access to json #288
  • What are global terms for file formats in bioinformatics workflows - revisit fileFormat #286
  • analysisType - GOenrichment #276
  • analysisType - polygenic score #273
  • need additional fileFormat values for imputed genotypes #264
  • Confirm list of "consortium" values in sageCommunity.json #230
  • Hi-C resolution #191
  • dependencies of values between keys #160
  • Add use case for copying annotations from one project to another #140
  • Add use case for uploading and annotating a new project #139
  • Add use case to create annotations #138
  • Clarify description of "organ" key term. #119
  • Make 'targetedGeneSequencing' assay description/source more generic. #117
  • Solution for handling multiple samples/values in annotation #107
  • Create tool/workflow annotations #83
  • Brain region complexities #64

Merged pull requests:

v6.1.1 (2017-12-19)

Full Changelog

Closed issues:

  • fileFormat - sdf #283
  • Create annotations to cover drug/compound screens #272
  • add value 'precuneus' to key 'tissue' (Brodmann area 7) #259
  • add R (script) as fileFormat #254
  • add tar as fileFormat #253
  • Resolve dataType for methylation and ChIPSeq #252
  • what dataType to go with assay=CHiP-seq? #244

Merged pull requests:

v6.0.0 (2017-11-07)

Full Changelog

Implemented enhancements:

Closed issues:

  • dataType for idats #268
  • CHiP-seq is spelled wrong #242

Merged pull requests:

v5.0.0 (2017-10-17)

Full Changelog

Implemented enhancements:

  • Automate changelog for releases #237
  • change all source = "Sage" to "Sage Bionetworks" #234
  • Update sageCommunity.json #241 (kdaily)
  • added fileFormat - bedgraph #240 (amapeters)

Merged pull requests:

  • Add in changelog.md #246 (kdaily)
  • Change source 'Sage' to 'Sage Bionetworks' #245 (kdaily)
  • correcting ChIPseq spelling #243 (allaway)
  • Script to normalize json files into a melted dataframe then merge by row checking to a synapse table #141 (teslajoy)

v4.1.1 (2017-10-11)

Full Changelog

Closed issues:

  • In experimentalData.json, link for "pancreas cancer" says "pancreatic cancer" #213
  • convert all http to https #192

Merged pull requests:

v3.1.0 (2017-09-06)

Full Changelog

Closed issues:

  • move code to synAnnotationUtils #182
  • switch to PR against a develop branch instead of master to prevent accidental changes before a release #181

Merged pull requests:

v2.1.2 (2017-08-17)

Full Changelog

Closed issues:

  • remove case, control from diagnosis, add cohort key to analysis, and define case control as a cohort values #185

Merged pull requests:

  • added boolean keys for multi-specimen and multi-individual #183 (kdaily)

v2.1.1 (2017-08-15)

Full Changelog

Implemented enhancements:

  • Rename 'projects' to 'modules' or something more generic #175

Merged pull requests:

v2.0.1 (2017-08-09)

Full Changelog

Merged pull requests:

v2.0.0 (2017-08-09)

Full Changelog

Implemented enhancements:

  • Revisit minified to determine what is needed #155

Closed issues:

  • Organize repo #71
  • platform-related metadata #42

Merged pull requests:

  • Rename sageCommunity_annotations.json to sage_community_annotations.json #176 (kdaily)
  • Proposal for reduced minified #161 (sgosline)

v1.4.1 (2017-08-08)

Full Changelog

Implemented enhancements:

  • Write integration test for json normalization funtion json2flatten() in json2synapse #169

Fixed bugs:

  • Write unit test for update table #172

Closed issues:

  • true false values as "non-string" documented as boolean in json files end-up missing in manifest #168

Merged pull requests:

  • changed special char ’ to ' causing error in string encode parsing - … #173 (teslajoy)
  • Added - 'channel' red and green #170 (amapeters)
  • Added fileFormat - idat #167 (amapeters)
  • Add confocalMicroscopy to assay #166 (xindiguo)
  • Added new values to modelSystemNameCommon and modelsSystemStrainNomen… #164 (ychae)
  • Combining dna and rna alignmentMethods #145 (amapeters)

v1.3.0 (2017-07-05)

Full Changelog

Merged pull requests:

  • changed naming convention and format of tool project json files (addi… #163 (teslajoy)

v1.2.0 (2017-06-27)

Full Changelog

Closed issues:

  • Link release version tags to table versions on synapse #157

Merged pull requests:

v1.1.0 (2017-06-13)

Full Changelog

Closed issues:

  • Establish release process and release numbering scheme #144

Merged pull requests:

  • added isGenomewideNetwork key to analysis #153 (ychae)
  • removed isGenomewideNetwork key from minified #152 (ychae)
  • added forebrain value for tissue key #148 (ychae)
  • Additional groups and studies #146 (amapeters)
  • Added Bolean flag to indicate if network is genomwide or single module #133 (amapeters)

v1.0.0 (2017-06-01)

Implemented enhancements:

  • Data-type specific annotations #57
  • remove some categories from main annotation #7

Closed issues:

  • consortia confusion #125
  • .gtf fileFormat #124
  • Add details for NGS library types (re: stranded, paired end) #123
  • Allow json2excel input to be url #121
  • Add descriptions for organ terms. #118
  • Write a script that converts list of dictionary objects into a dictionary with names as key #94
  • Remove old yml files #88
  • Add testing format #80
  • Schema freezes for releases #69
  • Come up with unified scheme for individual and sample identifiers #56
  • fileFormat consistency with powerpoint and excel #46
  • review analysis annotations #4
  • Adjust case #2

Merged pull requests:

* This Change Log was automatically generated by github_changelog_generator