v14.0.0

14.0.0 (2020-05-21)

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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

13.0.0 (2020-05-08)

Full Changelog

Closed issues:

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

Merged pull requests:

• Add MCSA study #599 (Aryllen)
• Schemaorg conversion v2 #598 (milen-sage)
• Remove never-used MODEL-AD studies #597 (bememea)
• Add IU to individualIdSource #596 (bememea)
• Update MODEL-AD rat study name #595 (bememea)
• Add and update MODEL-AD studies #589 (bememea)
• Add left and right hemispheres #588 (bememea)
• Add fileFormats mex and cloupe for 10x cellranger files #587 (Aryllen)
• Add CMC-PEC study #586 (cw-dvr8)
• Add mouse behavior assays #585 (bememea)
• Add TS-RNAseq study #583 (cw-dvr8)
• Add Sestan to individualIdSource #582 (cw-dvr8)
• Add UM-BTB to individualIdSource #581 (cw-dvr8)
• HiSeq1000 platform #580 (cw-dvr8)
• Retype chromatin amount #579 (cw-dvr8)
• Terms for immunoassays #578 (cw-dvr8)
• New individual ID sources #576 (cw-dvr8)
• New library prep #575 (cw-dvr8)
• Add CSF as tissue #574 (karawoo)
• Added new values to nucleicAcidSource #573 (cw-dvr8)
• New PEC study #571 (amapeters)

v12.2.0

12.2.0 (2020-03-04)

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Merged pull requests:

• Add Q Exactive HF to platform #570 (karawoo)
• New AD study #569 (amapeters)
• Add BannerSun as individualIdSource #568 (karawoo)
• Add new diagnoses #567 (karawoo)
• libraryPrep add STARR-Seq #566 (cw-dvr8)
• New AMP-AD study #565 (amapeters)
• Add PCRfree to libraryPrep #564 (cw-dvr8)
• assay: HPLC #563 (allaway)
• Add Emory to individualIdSource #562 (bememea)
• New study #561 (amapeters)
• New studies #560 (amapeters)
• Add script to update table #559 (karawoo)
• Add Infinium Omni2.5Exome-8 v1.3 to platform #554 (karawoo)

v12.1.0

12.1.0 (2020-02-03)

Full Changelog

Closed issues:

• Allow alternate capitalizations of boolean values #535

Merged pull requests:

• add platform value #558 (kelshmo)
• add two tissue terms #557 (kelshmo)
• Source update #556 (amapeters)
• Added UCSF to individualIdSource #555 (cw-dvr8)
• Added a description for the sex key #553 (cw-dvr8)
• Update source for orbitrap fusion #552 (karawoo)
• Add sc.rnaSeq to assays #551 (bememea)
• Add search engine output files as analysisType #549 (karawoo)
• Fixed typo in assay key #548 (cw-dvr8)
• Added platform = Q-Exactive Plus #547 (amapeters)
• Added platforms #546 (amapeters)
• Added Synapse table as file format #545 (sgosline)
• Update experimentalData.json #544 (allaway)
• add assay: photograph #543 (allaway)
• Add head of caudate nucleus #541 (karawoo)
• Remove boolean enumerated values #538 (karawoo)

v12.0.0

12.0.0 (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:

• Add manifest as a metadataType #540 (karawoo)
• Added definition for BrodmannArea #537 (amapeters)
• Add czi as fileFormat #536 (bememea)
• add Nf osi schema to develop branch #533 (sgosline)
• Library preparation method #532 (cw-dvr8)
• Update modelSystemName for MODEL-AD strains #531 (bememea)
• Add MODEL-AD teams to group key #530 (bememea)
• Add MODEL-AD studies #529 (bememea)
• Add MODEL-AD studies #527 (bememea)
• Reword sentence in contributing guide #526 (karawoo)
• Remove grant values #523 (karawoo)
• Add individualID description #522 (cw-dvr8)
• Added dataSubtype = normalized #521 (amapeters)
• added mouse behavior assays #518 (amapeters)
• Added assay = mRNAcounts, platform = NanostringnCounter_MouseADPanel #517 (amapeters)
• Updated treatmentType #514 (amapeters)
• Added assay = autoradiography #513 (amapeters)
• libraryPrepartionMethod value #509 (kelshmo)
• add type of proeomics assay #507 (kelshmo)
• add dicom #506 (allaway)
• added assay = chemistry panels #496 (amapeters)
• Added assay = electrochemiluminescence #495 (amapeters)

v11.0.0

11.0.0 (2019-07-16)

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:

• Organize modelSystemName #505 (bememea)
• fileFormat additions for PEC #504 (kelshmo)
• Organize files in schemaorg-conversion work #503 (karawoo)
• Add json schema definitions and sample schemas #502 (karawoo)
• Added more detailed in-code documentation regarding manifest generation and google api credentials #501 (milen-sage)
• Added manifest generation code #500 (milen-sage)
• JSONschema schemas generation from schema.org schemas #499 (milen-sage)
• add assays hplc-ec and whole-cell patch clamp #498 (allaway)
• added assay = immunofluorescence #493 (amapeters)
• Update assay #492 (bememea)
• Updated study #490 (bememea)
• Updated grant #489 (bememea)
• Updated modelSystemNames #488 (bememea)
• Add matrix market exchange format #487 (karawoo)
• fix array.json #486 (kdaily)
• Lint all json files in the repo #485 (karawoo)
• Fix test for duplicate values #484 (karawoo)
• Remove some duplicate values in study and fileFormat #483 (karawoo)
• Neuro terms for PEC #481 (kelshmo)
• Remove duplicate tissue annotations #480 (karawoo)
• Add metadataType annotation #479 (karawoo)
• Add assay: laser speckle imaging #478 (karawoo)
• Add readme for schema generation #477 (karawoo)
• Add a .gitignore for files that should not be committed to the repo #474 (karawoo)
• Remove .DS_Store file #473 (karawoo)
• More case fixes #472 (karawoo)
• added buffy coat to tissue&organ #471 (xdoan)
• Schema.org conversion utilities #469 (milen-sage)
• Added cellType - iPSC-derived glia #468 (amapeters)
• added milestone to report items, and removed study #463 (sgosline)
• CMC annotations from develop branch #462 (kelshmo)
• add failedQC annotation #460 (karawoo)
• add high content screen assay #459 (allaway)
• add antibody array assay #458 (allaway)
• Add GATK VQSR recal and tranches fileFormats #457 (sgosline)
• added GATK VQSR recal and tranches fileFormat #456 (xdoan)
• forgot to do pull request for read-pair #455 (sgosline)
• added Immunocytochemistry and real time PCR #454 (sgosline)
• made some updates for the container SOP for csbc #453 (sgosline)
• Add study description for JAX_APPPS1 #452 (karawoo)
• Add electrophysiology as dataType #451 (karawoo)
• Add electrophysiology assays LTP and LFP #450 (karawoo)
• Add more info on how to perform release #448 (karawoo)
• Add referenceSet to curatedData.json #439 (kelshmo)

v10.0.0

Change Log

10.0.0 (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:

• creating drug combination data type #445 (sgosline)
• Add "bodyPart" key and "head" value #444 (karawoo)
• reorganize group key #443 (kdaily)
• Add behavioral assays #438 (karawoo)
• Add ELISA as assay and immunoassay as dataType #437 (karawoo)
• Add some AMP-AD related annotation values #436 (karawoo)
• Add SRA file format #435 (karawoo)
• Update organ in experimentalData.json #434 (kelshmo)
• add pig to species #430 (allaway)
• consolidate Synodos #429 (allaway)
• Add "whole brain" as a tissue #428 (karawoo)
• Document annotations release process #427 (karawoo)
• Add clinical as a dataType #425 (karawoo)
• add sanger sequencing assay #423 (allaway)
• add file formats #422 (allaway)
• add datatype weight #418 (allaway)
• add resourcetype = report #416 (allaway)
• Fix typo in readLength description #415 (karawoo)
• new terms needed for drug studies #414 (sgosline)
• Added new keys to assay, platform, tissue, organ, tumorType; updated ngs.json to fix downstream annotation upload (via annotator) #413 (milen-sage)
• added value gz to fileFormat #410 (ychae)
• Amapeters patch 1 #403 (amapeters)
• added value iPSC-HiC to study in neuro #402 (ychae)
• Added value hic to fileFormat #400 (ychae)
• Added assay Positron Emission Tomography #399 (ychae)
• Move Development section of README to CONTRIBUTING.md #393 (karawoo)
• added NHP-Chimpanzee study to neuro #387 (ychae)
• added Pan troglodytes to species #386 (ychae)
• addition of cell Line term #291 (sgosline)

v9.0.0

Change Log

v9.0.0 (2018-08-21)

Full Changelog

Implemented enhancements:

• Added values to tissue #223 (ychae)
• Add whole genome optical imaging to assays #200 (kdaily)

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:

• Update CONTRIBUTING.md with file format guideline #412 (kdaily)
• updated NF terms #409 (sgosline)
• Additions to entries in species, assay, platform, organ in experimentalData.json; additions to tumorType in cancer.json #408 (milen-sage)
• Add unspecified tissue #407 (karawoo)
• Added embryonic stem cells to cellType #406 (milen-sage)
• Fix relative links in README.md #398 (karawoo)
• NF-related additions #396 (sgosline)
• Updated terms for JMML spore data #395 (sgosline)
• Added dataType - behavior process #389 (amapeters)
• Added contribution of species terms section #388 (ychae)
• added value dorsal pallium to tissue #385 (ychae)
• add value Enrichr, DEseq2, correct spelling of visualization #384 (allaway)
• add ssGSEA, GSVA #383 (allaway)
• Added value Ribo-Seq to assay #380 (ychae)
• added assay OxBS #379 (ychae)
• Add existing annotations to ontologies folder #377 (karawoo)
• Add value "Rush" to individualIdSource #376 (karawoo)
• Added value VZ/SVZ to tissue key #374 (ychae)
• Added tissue value cortical plate #373 (ychae)
• New and corrected compound names. #372 (allaway)
• Update CONTRIBUTING.md #370 (kdaily)
• added STAR alignment method #369 (allaway)
• added key terminal differentiation point to experimentalData.json #368 (ychae)
• Added value plasma to tissue key #367 (ychae)
• Add a variety of values to reflect incoming CSBC data #361 (sgosline)
• added 11 studies to neuro #360 (ychae)
• remove modelSystem #359 (allaway)
• added ngs analysis terms #358 (allaway)
• edited description of plink files #356 (ychae)
• Revise data, experimentalData and curatedData #355 (allaway)
• added additional software type #354 (sgosline)
• updated ngs.json to accommodate scRNA-Seq data #353 (sgosline)
• larger update to create networkType and update network annotations #352 (sgosline)
• chem.json #349 (allaway)
• added .sdf and RData formats #348 (allaway)
• add chemical input/outputs #347 (allaway)
• added values novelObjectRecognition and activePlaceAvoidance #342 (ychae)
• Added new study #296 (amapeters)

v8.0.0

v8.0.0 (2018-02-23)

Full Changelog

Implemented enhancements:

• updated analysis annotations #321 (blogsdon)

Merged pull requests:

• Develop #345 (kdaily)

v7.0.0

v7.0.0 (2018-02-23)

Full Changelog

Implemented enhancements:

• create a CONTRIBUTING.md #290
• clarify capitalization/style guide for keys and values #206
• Contributing #313 (kdaily)
• Added analysisType - DNAmethylationImputation #238 (amapeters)
• Added tissues #208 (amapeters)

Closed issues:

• harmonize capitilization of analysis values with source #336
• Add link to shiny App in README.md #331
• Add normalizationMethod terms to analysis #330
• 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:

• Develop #344 (kdaily)
• add drug terms best practices to contributing doc #343 (allaway)
• fixed capitalization and synced preferred names #337 (philerooski)
• Update inputDataType and outputDataType #335 (xindiguo)
• Update platform values' description #329 (xindiguo)
• Add 'imputed drug response' to outputDataType #328 (xindiguo)
• Add 'ontology' to inputDataType and outputDataType #327 (xindiguo)
• Add "pathway or network" #326 (xindiguo)
• Add 'gene list' to inputDataType & outputDataType #325 (xindiguo)
• Add 'functional screen' as inputDataType #324 (xindiguo)
• Develop #323 (xindiguo)
• add compoundDoseRange #322 (allaway)
• Update experimentalData.json #320 (kdaily)
• added variant detection #319 (sgosline)
• Update experimentalData.json #318 (kdaily)
• added sequence alignment #317 (sgosline)
• added - assay value "NOMeSeq' #316 (amapeters)
• Updated analysis annotations #315 (sgosline)
• added descriptions, and info on organization. #314 (kdaily)
• added clozapine to treatmentType #312 (philerooski)
• added new software types #311 (sgosline)
• changed spelling of alignment method description #310 (teslajoy)
• Added new study #307 (amapeters)
• v6.1.1 changelog #306 (teslajoy)
• added fileFormat - Sentrix descriptor file #303 (ychae)
• changed experimental data - key targetedGeneSeq #300 (kkdang)
• changed annotationVersion #299 (teslajoy)
• useful keywords to close issues #298 (teslajoy)
• Added assay-immunohistochemistry #293 (amapeters)
• added fileFormat - Python script #282 (ychae)
• analysisType - enrichmentAnalysis #281 (amapeters)
• add in polygenicRiskScores as an analysisType #280 (blogsdon)
• added assay - LC-MS #279 (amapeters)
• Added isConsortiumAnalysis key #275 (amapeters)
• Update experimentalData.json #269 (kdaily)
• added cellType monocyte-derived microglia #263 (kdaily)
• add iPSC-derived neuronal progenitor cell #262 (kdaily)
• add iPSC-derived neuron #261 (kdaily)
• Update neuro.json #247 (kdaily)