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Add proposed ontology for BIDSprov#70

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neurorepro wants to merge 164 commits intobids-standard:masterbids-standard/BEP028_BIDSprov:masterfrom neurorepro:conciseneurorepro/BEP028_BIDSprov:conciseCopy head branch name to clipboard

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Commits

Commits on Mar 5, 2020

• [ADD] a basic README

  

  Remi Adon

  committed
  a31fe6f

• [ADD] CLI to visualize prov files

  

  Remi Adon

  committed
  a3124e0

Commits on Mar 11, 2020

• init jsonld files for spm_default

  

  Remi Adon

  committed
  94aef72

Commits on Mar 19, 2020

• improve spm_default/realign.json

  

  Remi Adon

  committed
  4b27841

Commits on Mar 20, 2020

• [RM] types for parameters & simplify reading

  

  Remi Adon

  committed
  fd353b3

Commits on Mar 23, 2020

• mke all examples use a context.json at the root

  

  Remi Adon

  committed
  e09f052

• spm_default realign uses entity from copies

  

  Remi Adon

  committed
  611f757

• gitignore graphviz files

  

  Remi Adon

  committed
  09c4c0d

• [MV] context local URIs to remote URIs

  

  Remi Adon

  committed
  381c629

• realign.json more infos on SPM

  

  Remi Adon

  committed
  d69bae1

Commits on Mar 24, 2020

• [ADD] copy activity & explicit exp_dit in paths

  

  Remi Adon

  committed
  65d1874

• [ADD] entity link realign and coreg

  

  Remi Adon

  committed
  4b0a851

• [RM] auditory fmri for now, may restore this later

  

  Remi Adon

  committed
  4b8efca

• [ADD] type indexing for spm_default

  

  Remi Adon

  committed
  55e6434

• [RM] misleading references to bids namespace

  

  Remi Adon

  committed
  af26bec

• [RM] link to bids in context

  

  Remi Adon

  committed
  ff8a938

• [remove] exp_dir definition

  

  Remi Adon

  committed
  dc07d4c

• type indexing agents in copies.json

  

  Remi Adon

  committed
  c1630a7

• Merge pull request bids-standard#4 from Inria-Visages/spm_default

  Show description for 399cf66
  

  Rémi Adon

  authored
  399cf66

Commits on Mar 27, 2020

• define SPM Agent in realign.json

  

  Remi Adon

  committed
  c5317c0

• Merge branch 'master' of https://github.com/Inria-Visages/BIDS-prov into spm_default_v2

  

  Remi Adon

  committed
  4accc8d

• instatiate semgent activity in realign.json

  

  Remi Adon

  committed
  7fea7eb

Commits on Apr 3, 2020

• mutliple copies && ids instead of labels

  

  Remi Adon

  committed
  0c43331

• add coreg, segment & normalise

  

  Remi Adon

  committed
  b13788f

Commits on Apr 6, 2020

• [ADD] .svg file for spm default

  

  Remi Adon

  committed
  e2d6f12

• [ADD] smoothing on functional img

  

  Remi Adon

  committed
  3d6db8b

Commits on Apr 9, 2020

• [ADD] model estimation

  

  Remi Adon

  committed
  d150a5b

• add report to PDF

  

  Remi Adon

  committed
  f333a45

• reformat json files, graph is just a dict

  

  Remi Adon

  committed
  febf10a

• explicit name for copy and unzip

  

  Remi Adon

  committed
  c624b0e

• [ADD] list of features not in the spec

  

  Remi Adon

  committed
  d0547d7

Commits on Apr 10, 2020

• [ADD] issue template for proposals

  

  Remi Adon

  committed
  9d6179e

Commits on Apr 14, 2020

• Merge pull request bids-standard#9 from Inria-Visages/spm_default_v2

  Show description for c4f4124
  

  Rémi Adon

  authored
  c4f4124

Commits on Apr 15, 2020

• [UPDATE] new_features list

  

  Remi Adon

  committed
  d1a1398

Commits on Apr 16, 2020

• rename spm_default subfolder

  

  Remi Adon

  committed
  bcc709c

• [ADD] workflow & readme for fsl_default

  

  Remi Adon

  committed
  c911856

Commits on Apr 17, 2020

• first draft for fsl_default

  

  Remi Adon

  committed
  3b57597

• [ADD] detailed preprocessing and logs as markdown

  

  Remi Adon

  committed
  a538893

Commits on Jul 30, 2020

• start reformatting README as for a BEP proposal

  

  Rémi Adon

  authored
  e6054f5

• enrich "How to help" section in README

  

  Rémi Adon

  authored
  99c5e94

• fix typo in README

  

  Rémi Adon

  authored
  c640df9

• add NIDM weekly call section to README

  

  Rémi Adon

  authored
  5002bcd

Commits on Jul 31, 2020

• Merge branch 'master' of https://github.com/Inria-Visages/BIDS-prov

  remiadon

  committed
  9996f8b

• Update who is who + title

  cmaumet

  authored
  7d1e508

Commits on Aug 4, 2020

• add requirements to read and viz json-ld as prov

  cmaumet

  committed
  b0f0e86

• context for JSON-LD 1.1 with type indexing

  cmaumet

  authored
  349c464

• Add missing namespaces to identifiers

  cmaumet

  committed
  30fd87d

• Update to point to context defining type indexing

  cmaumet

  committed
  8eebfa1

• graph is records (as in context)

  cmaumet

  committed
  1629ee5

• Fix prov types

  cmaumet

  committed
  adfc5ed

• Add missing namespace in id

  cmaumet

  committed
  85d4476

• Removing front node info (not sure if that's fine with viz)

  cmaumet

  committed
  5bb6f8b

• Toy examples for viz

  cmaumet

  committed
  a790f84

• Code to vizualize json-ld 1.1 as prov graph

  cmaumet

  committed
  bd643ec

Commits on Aug 5, 2020

• Merge pull request bids-standard#25 from cmaumet/fsl_default

  Show description for 3a98a36
  

  Rémi Adon

  authored
  3a98a36

• start reformatting README as for a BEP proposal

  

  Rémi Adon

  authored and

  remiadon

  committed
  12ea852

• enrich "How to help" section in README

  

  Rémi Adon

  authored and

  remiadon

  committed
  92e9c19

• fix typo in README

  

  Rémi Adon

  authored and

  remiadon

  committed
  1ef476a

• add NIDM weekly call section to README

  

  Rémi Adon

  authored and

  remiadon

  committed
  eb26af1

• update requirements

  remiadon

  committed
  4002835

• Create CODE_OF_CONDUCT.md

  

  Rémi Adon

  authored
  9601006

• Merge pull request bids-standard#24 from cmaumet/context-type-indexing

  Show description for 1f12f7c
  

  Rémi Adon

  authored
  1f12f7c

• Create contributing.md

  

  Rémi Adon

  authored
  341a1fc

Commits on Aug 6, 2020

• restructure contributing.md

  remiadon

  committed
  9db45ba

• Create LICENSE

  

  Rémi Adon

  authored
  99db44c

• Update issue templates

  remiadon

  authored
  e8b968c

• Merge branch 'master' of https://github.com/Inria-Visages/BIDS-prov

  remiadon

  committed
  ffb0c76

Commits on Sep 10, 2020

• git ignore

  cmaumet

  committed
  8266f20

• update notebook

  cmaumet

  committed
  2a10347

• Merge branch 'fsl_default' of github.com:Inria-Visages/BIDS-prov into fsl_default

  cmaumet

  committed
  f47b5dc

• Merge branch 'fsl_default' of https://github.com/Inria-Visages/BIDS-prov into fsl_default

  remiadon

  committed
  5b1a190

• [ADD] code of conduct

  remiadon

  committed
  39a2610

• [ADD] contributors in README

  remiadon

  committed
  545abf3

Commits on Sep 11, 2020

• update contributors

  

  Rémi Adon

  authored
  68a9d91

Commits on Sep 15, 2020

• Typo

  cmaumet

  authored
  e5bb531

• Update info NIDM

  cmaumet

  authored
  4dce4c3

• Update credits

  cmaumet

  authored
  c63c477

• Update CoC info

  cmaumet

  authored
  6aa5fea

• Merge pull request bids-standard#26 from bids-standard/add-code-of-conduct

  Show description for 30d3e0c
  cmaumet

  authored
  30d3e0c

• Update template

  cmaumet

  authored
  63de9cf

• Update template

  cmaumet

  authored
  bd5dca9

• Update

  cmaumet

  authored
  7aefdae

• Merge pull request bids-standard#19 from bids-standard/spec_issue_template

  Show description for a3fd2ea
  cmaumet

  authored
  a3fd2ea

• Move issue template to corresponding folder

  cmaumet

  authored
  7745731

• Move to issue template folder

  cmaumet

  authored
  f236cd7

• Create spec_update.md

  

  Rémi Adon

  authored
  57c49ff

• create context for JSON-LD 1.0 with all elements of JSON-LD 1.1 context

  cmaumet

  committed
  4edf6e3

• Merge branch 'fsl_default' of https://github.com/bids-standard/BEP028_BIDSprov into fsl_default

  remiadon

  committed
  7563143

• scr @id to RRID

  remiadon

  committed
  c611ee9

• fix RRID

  cmaumet

  committed
  291c58d

• Update spec_update.md

  

  Rémi Adon

  authored
  245edc5

• Delete spec_update_issue_template.md

  

  Rémi Adon

  authored
  56cc083

• first working w3c graph

  remiadon

  committed
  108a6d1

Commits on Sep 17, 2020

• [RM] deprecated CODE_OF_CONDUCT

  remiadon

  committed
  711ba12

• Merge pull request bids-standard#27 from bids-standard/contributing

  Show description for e0c78c3
  

  Rémi Adon

  authored
  e0c78c3

Commits on Sep 18, 2020

• resolve conflicts

  cmaumet

  committed
  821f470

• Merge pull request bids-standard#20 from bids-standard/fsl_default

  Show description for 6527a3c
  cmaumet

  authored
  6527a3c

• Merge branch 'master' of github.com:Inria-Visages/BIDS-prov into lib

  cmaumet

  committed
  6db9a16

• Merge pull request bids-standard#30 from bids-standard/lib

  Show description for de0a189
  cmaumet

  authored
  de0a189

• Typo

  cmaumet

  authored
  513667a

• Fix conflict in merge

  cmaumet

  authored
  e228da7

• Update info on PRs

  cmaumet

  authored
  2672028

Commits on Sep 21, 2020

• [VIZ] handle single definition across multiple files

  remiadon

  committed
  243d8bd

Commits on Sep 22, 2020

• SPM coreg [FIX] inputs and [ADD] --omit-details flag to viz CLI

  remiadon

  committed
  7cc3727

• SPM shorten identifiers for readability

  remiadon

  committed
  8f41fab

• SPM : segment activity uses anat nii header entity

  remiadon

  committed
  c6542a5

Commits on Sep 25, 2020

• SPM : single SPM.mat node

  remiadon

  committed
  b3d891c

• SPM : [ADD] batch.m file

  remiadon

  committed
  4ed8159

• Merge pull request bids-standard#31 from bids-standard/lib

  Show description for 4fbf61f
  

  Rémi Adon

  authored
  4fbf61f

Commits on Oct 13, 2020

• fsl default : [FIX] dead nodes

  remiadon

  committed
  aa9e457

• fsl default : separate single subject workflow from group analysis workflow

  remiadon

  committed
  f5f90bf

• update fsl preprocessing.json, seems deprecated

  remiadon

  committed
  05cbbe0

• [RM] fsl preprocessing, deprecated

  remiadon

  committed
  af70a96

• clean fsl_default folder

  remiadon

  committed
  6e424dc

• fsl_default replace .png by generated graph

  remiadon

  committed
  1a13e3d

Commits on Oct 14, 2020

• [ADD] .png for spm_default

  remiadon

  committed
  636089c

• [ADD] isInfluencedBy in new_features

  remiadon

  committed
  76bd469

Commits on Oct 19, 2020

• Merge pull request bids-standard#37 from bids-standard/fsl_default_v2

  Show description for c297118
  

  Rémi Adon

  authored
  c297118

Commits on Oct 28, 2020

• first draft for fMRIprep

  remiadon

  committed
  ae0a67e

Commits on Nov 5, 2020

• simplify fmriprep example

  remiadon

  committed
  c23b1bd

• update fmriprep .png

  remiadon

  committed
  f0e7d56

• Merge pull request bids-standard#42 from bids-standard/fmri_prep

  Show description for f15381e
  

  Rémi Adon

  authored
  f15381e

Commits on Feb 3, 2021

• v0 for spm parser

  remiadon

  committed
  c882080

• [FIX] output production

  remiadon

  committed
  b6584cd

• black spm_parser

  remiadon

  committed
  c2a4c29

Commits on Feb 4, 2021

• [FIX] activity names

  remiadon

  committed
  4518748

Commits on Feb 8, 2021

• [ADD] first test for spm parser

  remiadon

  committed
  20eb527

• [ADD] CI for unittests

  remiadon

  committed
  1af7fb9

• [FIX] dependency inference

  remiadon

  committed
  f094136

Commits on Feb 9, 2021

• [FIX] refs to SPM

  remiadon

  committed
  46436ff

Commits on Feb 16, 2021

• [FIX] missing used refs

  remiadon

  committed
  eeb94c8

• SPM parser + viz in CI

  remiadon

  committed
  a8f473c

• SPM parser, context as option

  remiadon

  committed
  ac1b03a

Commits on Feb 18, 2021

• SPM Parser [RM] links between entities and SPM

  remiadon

  committed
  5f14a6c

• SPM Parser [FIX] short activity name

  remiadon

  committed
  434eeaf

Commits on Feb 19, 2021

• SPM parser link activities via close names AND reference numbers

  remiadon

  committed
  d979c3f

• Merge pull request bids-standard#50 from bids-standard/spm_parser

  Show description for 10a9c66
  

  Rémi Adon

  authored
  10a9c66

Commits on Mar 12, 2021

• SPM parser config is now external

  remiadon

  committed
  e1b9b92

• [FIX] CI for bids_prov.spm_parser

  remiadon

  committed
  489b8bb

• SPM default graph in config

  remiadon

  committed
  50e2d63

Commits on Mar 16, 2021

• spm_parser : hard coded mappings in yaml file

  remiadon

  committed
  4be118c

• [ADD] missing requirement

  remiadon

  committed
  40cdc59

Commits on Mar 18, 2021

• SPM [FIX] duplicate gunzipped files

  remiadon

  committed
  e9cd9ac

Commits on Mar 29, 2021

• SPM [ADD] predefined outputs in static config

  remiadon

  committed
  f152c15

Commits on Apr 1, 2021

• rename spm_config.py to avoid confusion

  remiadon

  committed
  cef3720

• [ADD] bids_prov/README

  remiadon

  committed
  56c7187

Commits on Apr 26, 2021

• fix: avoid overwriting used dependency in the presence of used entities

  cmaumet

  committed
  0b24cab

• Merge pull request bids-standard#54 from bids-standard/spm_parser_config

  Show description for a241773
  cmaumet

  authored
  a241773

• rename static_map

  cmaumet

  committed
  24e9fa9

Commits on Jun 10, 2021

• FIX - remove redundancy in README

  tiborauer

  authored
  6321abd

• FIX - typo in README

  tiborauer

  authored
  23585fc

• Merge pull request bids-standard#55 from tiborauer/patch-1

  Show description for 707ba2f
  cmaumet

  authored
  707ba2f

Commits on Jun 15, 2021

• SPM parser improve [DOC] and [RM] dead code

  remiadon

  committed
  c5ee92b

• SPM parser improve [DOC]

  remiadon

  committed
  179df7e

• [RM] reprecated closest_activity

  remiadon

  committed
  17da659

• spm_parser set prov:atLocation for activities with default outputs

  remiadon

  committed
  ebd8b85

Commits on Jun 18, 2021

• [RM] wasAttributedTo

  remiadon

  committed
  16cfc0a

• quick [FIX] spm_parser bug on multiline definitions

  remiadon

  committed
  564df3a

• Merge pull request bids-standard#62 from bids-standard/remove_wasAttributedTo

  Show description for 8ece8a5
  cmaumet

  authored
  8ece8a5

• SPM parser parser multilines

  remiadon

  committed
  fa0293c

• [FIX] added lines from merge

  remiadon

  committed
  49122ed

• Merge pull request bids-standard#64 from bids-standard/spm_parser_multilines

  Show description for 3c03d36
  cmaumet

  authored
  3c03d36

Commits on Nov 23, 2021

• Update meeting times

  cmaumet

  authored
  f09767c

Commits on Dec 4, 2021

• Add proposed ontology for BIDSprov

  

  Michael Dayan

  committed
  6e14507