Ricgraph - Research in context graph

Ricgraph - Research in context graph
With Ricgraph (Research in context graph), you can create a graph from research information that is stored in various source systems. This can be done for multiple organizations. You can explore this graph and discover relations you were not aware of. What if... we look at research information as a graph? We would have relations between objects, we would be able to "walk" from one object to another, and related objects would be neighbors. For example, starting with a researcher, the publications of this person are only one step away by following one edge, and other contributors to that publication are again one step (edge) away. Ricgraph has been developed because our university had a need to explore and visualize our researchers, their research results (e.g. publications, data sets, software packages), the teams, their collaborations, skills, projects, and their relations. By combining this information in one graph, it is possible to show research in context (hence the name). Ricgraph is a graph that uses nodes and edges to represent objects and their relations. It can be used to store, manipulate and read metadata of any object that has a relation to another object. Metadata from objects can be obtained from any source system you'd like. You run the harvest script for that system, and data will be imported in Ricgraph and will be combined automatically with data which is already there. Ricgraph provides several harvest scripts, and scripts for other sources can be written easily.

Provided tools & services

Ricgraph

Type
  • Software Library
Executable name
ricgraph.py

Ricgraph Explorer

Note: No URL was registered for this service (yet)
Type
  • Web Application

Script to call all harvest scripts

Type
  • Command-line Application
Executable name
batch_harvest.py

Script to harvest OpenAlex for Ricgraph

Type
  • Command-line Application
Executable name
harvest_openalex_to_ricgraph.py

Script to harvest the data repository Yoda for Ricgraph

Type
  • Command-line Application
Executable name
harvest_yoda_to_ricgraph.py

Script to harvest the Research Information System Pure for Ricgraph

Type
  • Command-line Application
Executable name
harvest_pure_to_ricgraph.py

Script to harvest the Research Software Directory for Ricgraph

Type
  • Command-line Application
Executable name
harvest_rsd_to_ricgraph.py

Script to harvest the Utrecht University staff pages for Ricgraph

Type
  • Command-line Application
Executable name
harvest_uustaffpages_to_ricgraph.py

References

Citation

Please use one of the above reference publications to cite the software, if you want to cite the software directly, you can use the following citation generated from the metadata:

  • Janssen, Rik D.T.
(2024) Ricgraph - Research in context graph v1.14 .
  • Utrecht University
.

Logs & Reviews

Name
Automatic software metadata validation report for Ricgraph - Research in context graph v1.14
Author
  • codemetapy validator using software.ttl
Date
2024-02-06 03:22:31
Review
Please consult the CLARIAH Software Metadata Requirements at https://github.com/CLARIAH/clariah-plus/blob/main/requirements/software-metadata-requirements.md for an in-depth explanation of any found problems

Validation of Ricgraph - Research in context graph v1.14 was successful (score=4/5), but there are some remarks which you may or may not want to address:

1. Info: Software source code *SHOULD* link to a continuous integration service that builds the software and runs the software's tests (This is missing in the metadata)
2. Info: A research domain *SHOULD* be expressed as a category using the NWO Research Fields vocabulary, if applicable (This is missing in the metadata)
Rating
★ ★ ★ ★ ☆
(log file starts at Tue Feb  6 03:22:14 UTC 2024)

[harvester info] --> Processing ricgraph (https://github.com/UtrechtUniversity/ricgraph) [Tue Feb  6 03:22:14 UTC 2024]

[harvester info] Git updating cached clone of https://github.com/UtrechtUniversity/ricgraph...

[harvester info] Found release v1.14

[harvester info] Using 'v1.14'

[harvester info] Git reference: v1.14

[harvester info] Scanning directory /tmp/codemeta-harvester.cache/ricgraph for harvestable resources...

[harvester info] found codemeta-harvest.json for ricgraph (md5sum e59d973de75a784571648d7b94cc3320); values in here take precendence over (override) those in later detection stages

[harvester info] found CITATION.cff for ricgraph, converting to codemeta

[harvester info] Looking for license....

[harvester info] Found license MIT

[harvester info] Getting contributors from git...

[harvester info] Getting top contributor from git...

[harvester info] Git top contributor Rik D.T. Janssen <121875841+RikDTJanssen@users.noreply.github.com> will be assigned as author (and maintainer) if none are found in the metadata

[harvester info] Extracting last and first commit date from git log....

[harvester info] Date created: 2023-01-10T20:04:11Z+0100, date modified: 2024-01-25T14:05:17Z+0100

[harvester info] Querying Github/GitLab API (https://github.com/UtrechtUniversity/ricgraph)

[harvester info] Adding URL for found README: README.md

[harvester info] Found releaseNotes

[harvester info] Querying Zenodo API for DOI (access token provided)...

[harvester info] Looking for TRL information in README.md...

[harvester info] Found TRL https://w3id.org/research-technology-readiness-levels#Level6LatePrototype

[harvester info] Looking for repostatus information in README.md...

[harvester info] Found repostatus https://www.repostatus.org/#active

[harvester info] Looking for continuous integration information in README.md...

[harvester info] Looking for documentation links in README.md...

[harvester info] Falling back to git tag (v1.14) if no version number is specified...

[harvester info] Inferring repostatus information from git activity (used only as a fallback if not explicitly provided)...

[harvester info] Inferred repostatus https://www.repostatus.org/#active

[harvester info] Looking for repostatus information in README.md in master branch...

[harvester info] Found repostatus (master branch) https://www.repostatus.org/#active

[harvester info] Reconciliating: codemetapy  --baseuri https://tools.clariah.nl --baseuri https://tools.clariah.nl --includecontext --addcontext https://w3id.org/nwo-research-fields --addcontext https://w3id.org/research-technology-readiness-levels --addcontextgraph https://vocabs.dariah.eu/rest/v1/tadirah/data?format=text/turtle --trl --identifier "ricgraph" --codeRepository "https://github.com/UtrechtUniversity/ricgraph" --validate /etc/software.ttl --released --enrich --textv "Please consult the CLARIAH Software Metadata Requirements at https://github.com/CLARIAH/clariah-plus/blob/main/requirements/software-metadata-requirements.md for an in-depth explanation of any found problems" -O /tmp/out/ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/99-version.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/99-repostatus.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/90-authors.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/43-releasenotes.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/41-readme.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/40-gitapi.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/39-gitdate.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/32-contributors.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/29-license.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/12-citationcff.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/11-trl.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/11-repostatus.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/10-harvest.ricgraph.codemeta.json /tmp/codemeta-harvester.cache//tmp/05-repostatus.ricgraph.codemeta.json 

-- begin log --

Passed 14 files/sources but specified 0 input types! Automatically guessing types...

Detected input types: [('/tmp/codemeta-harvester.cache//tmp/99-version.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/99-repostatus.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/90-authors.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/43-releasenotes.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/41-readme.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/40-gitapi.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/39-gitdate.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/32-contributors.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/29-license.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/12-citationcff.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/11-trl.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/11-repostatus.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/10-harvest.ricgraph.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/05-repostatus.ricgraph.codemeta.json', 'json')]

Adding to contextgraph: /tmp/turtle

Initial URI automatically generated, may be overriden later: https://tools.clariah.nl/ricgraph

Processing source #1 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/99-version.ricgraph.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] processed 1 new triples, total is now 2

Processing source #2 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/99-repostatus.ricgraph.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] processed 1 new triples, total is now 3

Processing source #3 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/90-authors.ricgraph.codemeta.json

    Found main resource with URI https://tools.clariah.nl/ricgraph.topcontributor/snapshot

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] processed 8 new triples, total is now 10

Processing source #4 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/43-releasenotes.ricgraph.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] processed 2 new triples, total is now 12

Processing source #5 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/41-readme.ricgraph.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] processed 1 new triples, total is now 13

Processing source #6 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/40-gitapi.ricgraph.codemeta.json

    Found main resource with URI https://tools.clariah.nl/ricgraph/snapshot

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] processed 30 new triples, total is now 42

Processing source #7 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/39-gitdate.ricgraph.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] overriding old http://schema.org/dateCreated (2023-01-10T19:02:05Z -> 2023-01-10T20:04:11Z+0100)

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] overriding old http://schema.org/dateModified (2024-02-01T12:30:20Z -> 2024-01-25T14:05:17Z+0100)

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] processed 2 new triples, total is now 42

Processing source #8 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/32-contributors.ricgraph.codemeta.json

    Found main resource with URI https://tools.clariah.nl/ricgraph.contributors/snapshot

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] processed 14 new triples, total is now 51

Processing source #9 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/29-license.ricgraph.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] overriding old http://schema.org/license (http://spdx.org/licenses/MIT -> MIT)

[CODEMETA CORRECTION (https://tools.clariah.nl/ricgraph)] automatically converting license to spdx URI

[CODEMETA COMPOSITION (https://tools.clariah.nl/ricgraph)] processed 1 new triples, total is now 51

Processing source #10 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/12-citationcff.ricgraph.codemeta.json

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/author (https://tools.clariah.nl/stub/H4473eab0d406f67f -> https://tools.clariah.nl/stub/H-2a1fdb52d23a9351)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/description (Ricgraph - Research in context graph -> With Ricgraph (Research in context graph), you can create a graph from research information that is stored in various source systems. This can be done for multiple organizations. You can explore this graph and discover relations you were not aware of.

What if... we look at research information as a graph? We would have relations between objects, we would be able to "walk" from one object to another, and related objects would be neighbors. For example, starting with a researcher, the publications of this person are only one step away by following one edge, and other contributors to that publication are again one step (edge) away.

Ricgraph has been developed because our university had a need to explore and visualize our researchers, their research results (e.g. publications, data sets, software packages), the teams, their collaborations, skills, projects, and their relations. By combining this information in one graph, it is possible to show research in context (hence the name).

Ricgraph is a graph that uses nodes and edges to represent objects and their relations. It can be used to store, manipulate and read metadata of any object that has a relation to another object. Metadata from objects can be obtained from any source system you'd like. You run the harvest script for that system, and data will be imported in Ricgraph and will be combined automatically with data which is already there. Ricgraph provides several harvest scripts, and scripts for other sources can be written easily.)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (ricgraph-explorer -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (linked-data -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (data-harvesting -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (harvest-data -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (metadata -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (utrecht-university -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (data-enrichment -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (enrichment -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (knowledge-graph -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (harvest -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (ricgraph -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (visualization -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (graph -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (research-in-context-graph -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (harvester -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/keywords (graph-database -> Ricgraph)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/license (http://spdx.org/licenses/MIT -> https://spdx.org/licenses/MIT)

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] overriding old http://schema.org/name (ricgraph -> Ricgraph - Research in context graph)

[CODEMETA CORRECTION (https://doi.org/10.5281/zenodo.7524314)] automatically converting spdx license URI from https:// to http:///

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] processed 30 new triples, total is now 58

Processing source #11 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/11-trl.ricgraph.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] processed 1 new triples, total is now 59

Processing source #12 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/11-repostatus.ricgraph.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] processed 1 new triples, total is now 59

Processing source #13 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/10-harvest.ricgraph.codemeta.json

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] processed 73 new triples, total is now 129

Processing source #14 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/05-repostatus.ricgraph.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/ricgraph

[CODEMETA COMPOSITION (https://doi.org/10.5281/zenodo.7524314)] processed 1 new triples, total is now 129

Remapping URI to (possibly) new identifier and version component: https://tools.clariah.nl/ricgraph -> https://tools.clariah.nl/ricgraph/v1.14

[CODEMETA VALIDATION (ricgraph)] done

[CODEMETA ENRICHMENT (ricgraph)] automatically adding runtimePlatform Python derived from programmingLanguage Python

[CODEMETA ENRICHMENT (ricgraph)] considering first author as maintainer

VALIDATION https://tools.clariah.nl/ricgraph/v1.14 #1: Info: Software source code *SHOULD* link to a continuous integration service that builds the software and runs the software's tests (This is missing in the metadata)

VALIDATION https://tools.clariah.nl/ricgraph/v1.14 #2: Info: A research domain *SHOULD* be expressed as a category using the NWO Research Fields vocabulary, if applicable (This is missing in the metadata)

-- end log --

[harvester info] Output written to /tmp/out/ricgraph.codemeta.json

[harvester info] <-- Finished processing ricgraph (https://github.com/UtrechtUniversity/ricgraph) [Tue Feb  6 03:22:31 UTC 2024]

        

Metadata Properties

Version
v1.14 (release notes)
Interface types
  • Command-line Application
  • Software Library
  • Web Application
Software website
Source code repository
 https://github.com/UtrechtUniversity/ricgraph  Stars are an indicator of the popularity of this project on GitHub
Category
  • Analyzing
  • Browsing
  • Capturing
  • Discovering
  • Enriching
  • Exploration
  • Information Retrieval
  • Storing
Keywords
  • Data enrichment
  • Data harvesting
  • Data linking
  • Graph
  • Graph database
  • Knowledge graph
  • Linked data
  • Metadata
  • Research in context graph
  • Ricgraph
  • Ricgraph Explorer
  • Utrecht University
Development Status
  • 6 - Late prototype: Technology demonstrated in target setting, end-users adopt it for testing purposes.
  • Active: The project has reached a stable, usable state and is being actively developed.
Issue Tracker (Support)
https://github.com/UtrechtUniversity/ricgraph/issues  The number of open issues on the issue tracker  The number of closes issues on the issue tracker
Documentation
License
Author(s)
  •   Rik D.T. Janssen (Utrecht University)
Maintainer(s)
  •   Rik D.T. Janssen (Utrecht University)
Contributor(s)
Producer
Funder
  •   Utrecht University
Programming Language
  • Python
Runtime Platform
  • Python
Software dependencies
  • flask
  • markupsafe
  • neo4j
  • numpy
  • pandas
  • py2neo
  • pyalex
  • ratelimit
  • requests
  • sickle
  • xmltodict
Metadata validation
★ ★ ★ ★ ☆
Created
2023-01-10 20:04:11 +0100
Last modified
2024-01-25 14:05:17 +0100  Last commit (main branch). Gives an indication of project development activity and rough indication of how up-to-date the latest release is.  Number of commits since the last release. Gives an indication of project development activity and rough indication of how up-to-date the latest release is.