[DATALAD RUNCMD] Extract new dataset metadata from Gliem-Pavic tabby …

…records and add catalog entry

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "python code/process_subdirectory.py data UKD/Gliem-Pavic --dataset-type other --add-to-catalog --hide-access-request",
 "dsid": "010ebda1-06c2-4656-928d-b2a8d826a165",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [
  "inputs/*"
 ],
 "outputs": [
  "catalog/*"
 ],
 "pwd": "."
}
^^^ Do not change lines above ^^^

catalog/metadata/1015ed7c-0a3d-4dfc-9c4f-11fe71673a41/2b19531d70a86026323d94fee4ea7ead3c326023/0fd/36ebc9dad4d6af6ba7612a7da1e09.json

@@ -0,0 +1 @@
+{"type": "dataset", "dataset_id": "1015ed7c-0a3d-4dfc-9c4f-11fe71673a41", "dataset_version": "2b19531d70a86026323d94fee4ea7ead3c326023", "children": [{"type": "directory", "name": "FZJ", "path": "FZJ"}, {"type": "directory", "name": "UKD", "path": "UKD"}], "metadata_sources": {"key_source_map": {"type": ["catalog_core"], "dataset_id": ["catalog_core"], "dataset_version": ["catalog_core"], "url": ["catalog_core", "tabby"], "authors": ["tabby"], "name": ["tabby"], "description": ["tabby"], "keywords": ["tabby"], "funding": ["tabby"], "subdatasets": ["tabby"], "additional_display": ["tabby"]}, "sources": [{"source_name": "catalog_core", "source_version": "1", "source_parameter": {}, "source_time": 1713196244.289572, "agent_email": "t.heunis@fz-juelich.de", "agent_name": "Tosca Heunis"}, {"source_name": "tabby", "source_version": "0.1.0", "source_parameter": {}, "source_time": 1713196244.324001, "agent_name": "Tosca Heunis", "agent_email": "t.heunis@fz-juelich.de"}]}, "url": ["ssh://git@github.com/~/abcd-j/data.git", "https://www.abcd-j.de/", "https://github.com/abcd-j/data.git"], "authors": [{"name": "ABCD-J Research Consortium"}], "name": "The ABCD-J Data Catalog", "description": "This data catalog contains datasets from the ABCD-J research community project, officially titled \u201cVerbundprojekt: Accessing Behavior for Clinical Data and Joint usage (ABCD-J) - Eine Plattform f\u00fcr Verhaltensmarker der digitalen Neuromedizin in NRW\u201d. This project is a collaboration between five research institutions in the German state of North Rhine-Westphalia: University Clinic RWTH Aachen, University Clinic Bonn, University Clinic K\u00f6ln, University Clinic D\u00fcsseldorf and Research Centre J\u00fclich. The overarching goal of ABCD-J is to elevate existing technical solutions for research practice adoption. From the social perspective, the ABCD-J project aims to promote and facilitate collaboration between multiple research centres, while from the technical perspective the project will accelerate research through homogenization of workflows and processes, with particular emphasis on digital biomarker development.", "keywords": ["Aachen", "Bonn", "Cologne", "D\u00fcsseldorf", "J\u00fclich", "Collaboration", "Research", "Open data", "FAIR", "Biomarker", "Clinical", "Behaviour"], "funding": [{"@type": "schema:Grant", "name": "MKW-NRW: Ministerium f\u00fcr Kultur und Wissenschaft des Landes Nordrhein-Westfalen", "identifier": "Kooperationsplattformen 2022: KP22-106A", "schema:url": "https://www.mkw.nrw/"}], "subdatasets": [{"dataset_id": "3f8a45c0-08fc-479c-b561-cb6f744d2b5c", "dataset_version": "32f3303308c89b037fe1700547348470539a30cb", "dataset_path": "FZJ/jumax", "dataset_url": null, "dirs_from_path": ["FZJ", "jumax"]}, {"dataset_id": "0036b2c6-f131-4660-9ef9-945087ad02d3", "dataset_version": "1139b4c82d7ecd0d9ab25bf4c00ec2c06461d6da", "dataset_path": "FZJ/movies", "dataset_url": null, "dirs_from_path": ["FZJ", "movies"]}, {"dataset_id": "db7592d0-6206-5684-a29c-8059a6033241", "dataset_version": "0.1.0", "dataset_path": "UKD/ocr-PIRA-cohort", "dataset_url": null, "dirs_from_path": ["UKD", "ocr-PIRA-cohort"]}, {"dataset_id": "372e66b3-e654-4a0f-ba4c-6394bf314f2f", "dataset_version": "d468e9a9455b38b959db34bc5335fd66e42b2884", "dataset_path": "FZJ/EMA_Pilot", "dataset_url": null, "dirs_from_path": ["FZJ", "EMA_Pilot"]}, {"dataset_id": "d72933c1-a660-5970-8bfd-48fcdac59dc5", "dataset_version": "latest", "dataset_path": "UKD/Gliem-Pavic", "dataset_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167274", "dirs_from_path": ["UKD", "Gliem-Pavic"]}], "additional_display": [{"name": "ABCD-J", "icon": "fa-solid fa-graduation-cap", "content": {"@context": {"homepage": "https://schema.org/mainEntityOfPage", "data controller": "https://w3id.org/dpv#hasDataController", "sample (organism)": "https://openminds.ebrains.eu/controlledTerms/Species", "sample (organism part)": "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation", "used for": "http://www.w3.org/ns/prov#hadUsage"}, "homepage": {"@type": "https://schema.org/URL", "@value": "https://www.abcd-j.de/"}}}]}

catalog/metadata/1015ed7c-0a3d-4dfc-9c4f-11fe71673a41/2b19531d70a86026323d94fee4ea7ead3c326023/212/8535a72dbfd8f80b219168daa2128.json

@@ -0,0 +1 @@
+{"type": "directory", "dataset_id": "1015ed7c-0a3d-4dfc-9c4f-11fe71673a41", "dataset_version": "2b19531d70a86026323d94fee4ea7ead3c326023", "children": [{"type": "dataset", "name": "ocr-PIRA-cohort", "path": "UKD/ocr-PIRA-cohort", "dataset_id": "db7592d0-6206-5684-a29c-8059a6033241", "dataset_version": "0.1.0"}, {"type": "dataset", "name": "Gliem-Pavic", "path": "UKD/Gliem-Pavic", "dataset_id": "d72933c1-a660-5970-8bfd-48fcdac59dc5", "dataset_version": "latest"}], "path": "UKD", "name": "UKD"}

catalog/metadata/1015ed7c-0a3d-4dfc-9c4f-11fe71673a41/2b19531d70a86026323d94fee4ea7ead3c326023/config.json

@@ -0,0 +1 @@
+{"catalog_name": "ABCDJ Catalog", "logo_path": "abcdj_catalog_logo.svg", "link_color": "#151868", "link_hover_color": "#3d43d7", "social_links": {"about": "https://datalad.org/", "documentation": "https://datalad.org/", "github": "https://github.com/datalad/", "x": "https://twitter.com/datalad"}, "dataset_options": {"default_tab": "subdatasets", "include_metadata_export": false}, "property_sources": {"dataset": {"dataset_id": {"rule": "single", "source": "catalog_core"}, "dataset_version": {"rule": "single", "source": "catalog_core"}, "type": {"rule": "single", "source": "catalog_core"}, "children": {"rule": "merge", "source": "any"}, "name": {"rule": "single", "source": "tabby"}, "short_name": {}, "description": {"rule": "single", "source": "tabby"}, "doi": {"rule": "single", "source": "tabby"}, "url": {"rule": "merge", "source": "any"}, "authors": {"rule": "priority", "source": ["tabby", "catalog_core"]}, "keywords": {"rule": "merge", "source": "any"}, "license": {}, "funding": {"rule": "merge", "source": "any"}, "publications": {"rule": "merge", "source": "any"}, "subdatasets": {"rule": "merge", "source": "any"}, "additional_display": {"rule": "merge", "source": "any"}, "top_display": {"rule": "merge", "source": "any"}}}}

catalog/metadata/1015ed7c-0a3d-4dfc-9c4f-11fe71673a41/2b19531d70a86026323d94fee4ea7ead3c326023/db7/21c0a4019bc482cf3466305431951.json

@@ -0,0 +1 @@
+{"type": "directory", "dataset_id": "1015ed7c-0a3d-4dfc-9c4f-11fe71673a41", "dataset_version": "2b19531d70a86026323d94fee4ea7ead3c326023", "children": [{"type": "dataset", "name": "jumax", "path": "FZJ/jumax", "dataset_id": "3f8a45c0-08fc-479c-b561-cb6f744d2b5c", "dataset_version": "32f3303308c89b037fe1700547348470539a30cb"}, {"type": "dataset", "name": "movies", "path": "FZJ/movies", "dataset_id": "0036b2c6-f131-4660-9ef9-945087ad02d3", "dataset_version": "1139b4c82d7ecd0d9ab25bf4c00ec2c06461d6da"}, {"type": "dataset", "name": "EMA_Pilot", "path": "FZJ/EMA_Pilot", "dataset_id": "372e66b3-e654-4a0f-ba4c-6394bf314f2f", "dataset_version": "d468e9a9455b38b959db34bc5335fd66e42b2884"}], "path": "FZJ", "name": "FZJ"}

catalog/metadata/d72933c1-a660-5970-8bfd-48fcdac59dc5/latest/0f3/1ad05527320283f5678af43956067.json

@@ -0,0 +1 @@
+{"type": "dataset", "dataset_id": "d72933c1-a660-5970-8bfd-48fcdac59dc5", "dataset_version": "latest", "children": [{"type": "directory", "name": "GSE167274_RAW", "path": "GSE167274_RAW", "dataset_id": "d72933c1-a660-5970-8bfd-48fcdac59dc5", "dataset_version": "latest"}], "metadata_sources": {"key_source_map": {"name": ["tabby"], "license": ["tabby"], "description": ["tabby"], "authors": ["tabby"], "keywords": ["tabby"], "funding": ["tabby"], "publications": ["tabby"], "access_request_contact": ["tabby"], "url": ["tabby"], "additional_display": ["tabby"]}, "sources": [{"source_name": "tabby", "source_version": "0.1.0", "source_parameter": {}, "source_time": 1713196243.074449, "agent_name": "Tosca Heunis", "agent_email": "t.heunis@fz-juelich.de"}]}, "name": "Microglia contributes to remyelination in cerebral but not spinal cord ischemia", "license": {"name": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html", "url": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html"}, "description": "Comparison of murine samples after spinal cord injury and cerebral photothrombosis. The goal is to compare cell recruitment and gene/pathway regulation betwen both brain and spinal cord after ischemic injury.", "authors": [{"email": "michael.gliem@med.uni-duesseldorf.de", "name": "Michael Gliem"}, {"email": "goran.pavic@med.uni-duesseldorf.de", "name": "Goran Pavic", "identifiers": [{"name": "ORCID", "identifier": "0000-0002-8104-1108"}]}], "keywords": ["brain", "spinal cord", "stroke", "spinal cord injury", "photothrombosis"], "funding": [{"@type": "schema:Grant", "name": "DFG", "identifier": "JA 690/8-1"}, {"@type": "schema:Grant", "name": "DFG", "identifier": "ME 3283/13-1"}], "publications": [{"@type": "schema:CreativeWork", "datePublished": "2021-08-14", "doi": "10.1002/glia.24068", "schema:url": "https://onlinelibrary.wiley.com/doi/10.1002/glia.24068", "title": "Pavic, G., et al., Microglia contributes to remyelination in cerebral but not spinal cord ischemia. Glia, 2021. 69(11): p. 2739-2751.", "authors": []}], "access_request_contact": {"givenName": "Michael", "familyName": "Gliem", "email": "michael.gliem@med.uni-duesseldorf.de"}, "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167274", "additional_display": [{"name": "ABCD-J", "icon": "fa-solid fa-graduation-cap", "content": {"@context": {"homepage": "https://schema.org/mainEntityOfPage", "data controller": "https://w3id.org/dpv#hasDataController", "sample (organism)": "https://openminds.ebrains.eu/controlledTerms/Species", "sample (organism part)": "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation", "used for": "http://www.w3.org/ns/prov#hadUsage"}, "sample (organism)": {"@type": "https://openminds.ebrains.eu/controlledTerms/Species", "name": "Mus musculus", "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/NCBITaxon_10090", "synonym": "house mouse"}, "sample (organism part)": [{"@type": "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation", "name": "brain", "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/UBERON_0000955"}, {"@type": "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation", "name": "spinal cord", "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/UBERON_0002240"}], "homepage": {"@type": "https://schema.org/URL", "@value": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167274"}, "data controller": [{"@type": "https://schema.org/Person", "email": "michael.gliem@med.uni-duesseldorf.de", "name": "Michael Gliem"}, {"@type": "https://schema.org/Person", "email": "goran.pavic@med.uni-duesseldorf.de", "name": "Goran Pavic"}], "used for": {"@type": "https://schema.org/Thing", "name": "Microarray analysis", "url": "https://onlinelibrary.wiley.com/doi/10.1002/glia.24068", "description": "Main analysis for publishing in GLIA"}}}]}

catalog/metadata/d72933c1-a660-5970-8bfd-48fcdac59dc5/latest/config.json

@@ -0,0 +1 @@
+{"catalog_name": "ABCDJ Catalog", "logo_path": "abcdj_catalog_logo.svg", "link_color": "#151868", "link_hover_color": "#3d43d7", "social_links": {"about": "https://datalad.org/", "documentation": "https://datalad.org/", "github": "https://github.com/datalad/", "x": "https://twitter.com/datalad"}, "dataset_options": {"default_tab": "content", "include_metadata_export": false, "include_access_request": false}, "property_sources": {"dataset": {"dataset_id": {"rule": "single", "source": "catalog_core"}, "dataset_version": {"rule": "single", "source": "catalog_core"}, "type": {"rule": "single", "source": "catalog_core"}, "children": {"rule": "merge", "source": "any"}, "name": {"rule": "single", "source": "tabby"}, "short_name": {}, "description": {"rule": "single", "source": "tabby"}, "doi": {"rule": "single", "source": "tabby"}, "url": {"rule": "merge", "source": "any"}, "authors": {"rule": "priority", "source": ["tabby", "catalog_core"]}, "keywords": {"rule": "merge", "source": "any"}, "license": {}, "funding": {"rule": "merge", "source": "any"}, "publications": {"rule": "merge", "source": "any"}, "subdatasets": {"rule": "merge", "source": "any"}, "additional_display": {"rule": "merge", "source": "any"}, "top_display": {"rule": "merge", "source": "any"}}}}

catalog/metadata/super.json

@@ -1 +1 @@
-{"dataset_id": "1015ed7c-0a3d-4dfc-9c4f-11fe71673a41", "dataset_version": "053d810a0ef46745823313b0e854112a3e287a71"}
+{"dataset_id": "1015ed7c-0a3d-4dfc-9c4f-11fe71673a41", "dataset_version": "2b19531d70a86026323d94fee4ea7ead3c326023"}