From db25cbf1d397c8daf44ca110f736947db7c0592f Mon Sep 17 00:00:00 2001 From: deepakunni3 Date: Thu, 3 Feb 2022 15:09:49 +0100 Subject: [PATCH 01/28] Add KGX to README.md --- README.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/README.md b/README.md index 84fd9b4..36ab400 100644 --- a/README.md +++ b/README.md @@ -79,6 +79,20 @@ Furthermore, this repository might serve as a **cristallization point for a comm - A high level simple way of specifying data models, optionally enhanced with semantic annotations - A python framework for compiling these data models to json-ld, json-schema, shex, shacl, owl, sql-ddl - A python framework for data conversion and validation, as well as generated Python dataclasses +- [KGX](https://github.com/biolink/kgx) - Library for building and exchanging knowledge graphs + - docs: https://kgx.readthedocs.io/ + - features: + - Load graphs into an in-memory model to facilitate data integration, validation, and graph operations + - Provides an easy way to bring data into Biolink Model, a a high-level data model for biomedical knowledge graphs + - The core data structure is a Property Graph (PG), represented internally using a `networkx.MultiDiGraph` + - Supports various input and output formats including, + - RDF serializations + - SPARQL endpoints + - Neo4j endpoints + - CSV/TSV and JSON + - OWL + - OBOGraph JSON format + - SSSOM - [Macleod](https://github.com/thahmann/macleod) – Ontology development environment for Common Logic (CL) - features: - Translating a CLIF file to formats supported by FOL reasoners From 5b3fec81b4e1a76c3bae91ccd4be6653654684a0 Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Fri, 4 Feb 2022 00:47:33 +0100 Subject: [PATCH 02/28] fix alphabetic sorting --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 36ab400..b47caef 100644 --- a/README.md +++ b/README.md @@ -74,11 +74,6 @@ Furthermore, this repository might serve as a **cristallization point for a comm - import paths from note-taking tools, such as Roam Research - usage in [MkRefs](https://github.com/DerwenAI/mkrefs) to add semantic features into MkDocs so that open source projects can federate bibliographies, shared glossaries, etc. - kglab team provides hands-on workshops at technology conferences for people to gain experience with these different graph approaches -- [LinkML](https://github.com/linkml/linkml) – Linked Open Data Modeling Language - - features: - - A high level simple way of specifying data models, optionally enhanced with semantic annotations - - A python framework for compiling these data models to json-ld, json-schema, shex, shacl, owl, sql-ddl - - A python framework for data conversion and validation, as well as generated Python dataclasses - [KGX](https://github.com/biolink/kgx) - Library for building and exchanging knowledge graphs - docs: https://kgx.readthedocs.io/ - features: @@ -93,6 +88,11 @@ Furthermore, this repository might serve as a **cristallization point for a comm - OWL - OBOGraph JSON format - SSSOM +- [LinkML](https://github.com/linkml/linkml) – Linked Open Data Modeling Language + - features: + - A high level simple way of specifying data models, optionally enhanced with semantic annotations + - A python framework for compiling these data models to json-ld, json-schema, shex, shacl, owl, sql-ddl + - A python framework for data conversion and validation, as well as generated Python dataclasses - [Macleod](https://github.com/thahmann/macleod) – Ontology development environment for Common Logic (CL) - features: - Translating a CLIF file to formats supported by FOL reasoners From 7ca9c67893d6d53ed0efb466107b506f19e78cf0 Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Fri, 4 Feb 2022 10:18:22 +0100 Subject: [PATCH 03/28] insert joint-community-badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index b47caef..b0c19af 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,4 @@ +[![join community](https://pysemtec.org/img/join-community.svg "join community")](https://pysemtec.org) # Semantic Python Overview This repository aims to collect and curate a list of projects which are related both to python and semantic technologies (RDF, OWL, SPARQL, Reasoning, ...). It is inspired by collections like [awesome lists](https://github.com/sindresorhus/awesome#readme). The list might be incomplete and biased, due to the limited knowledge of its authors. Improvements are very welcome. Feel free to file an issue or a pull request. Every section is alphabetically sorted. From 8b5d06dca26dd7daf660063333eb8a810a46aec5 Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Fri, 4 Feb 2022 21:17:21 +0100 Subject: [PATCH 04/28] add awesome-ontology maintained by @ozekik --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index b0c19af..1488747 100644 --- a/README.md +++ b/README.md @@ -228,6 +228,7 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma ## Further Projects / Links +- [ontology](https://github.com/ozekik/awesome-ontology) – A curated list of ontology things (with some python-related entries) - [awesome-semantic-web#python](https://github.com/semantalytics/awesome-semantic-web#python) Python section of awesome list for semantic-web-related projects - [github-semantic-web-python](https://github.com/topics/semantic-web?l=python) – github project search with `topic=semantic-web` and `language=python` - [Pywikibot](https://github.com/wikimedia/pywikibot) From 349168a346af566e9d474fc056ed14ba01c0585c Mon Sep 17 00:00:00 2001 From: Open Risk Date: Mon, 14 Feb 2022 16:25:53 +0100 Subject: [PATCH 05/28] Update README.md --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 1488747..dc03887 100644 --- a/README.md +++ b/README.md @@ -153,6 +153,11 @@ Furthermore, this repository might serve as a **cristallization point for a comm - docs: https://pronto.readthedocs.io/en/latest/api.html - [PyFuseki](https://github.com/yubinCloud/pyfuseki) – Library that interact with Jena Fuseki (SPARQL server): - docs: https://yubincloud.github.io/pyfuseki/ +- [PyLD](https://github.com/digitalbazaar/pyld) - A JSON-LD processor written in Python + - conforms: + - JSON-LD 1.1, W3C Candidate Recommendation, 2019-12-12 or newer + - JSON-LD 1.1 Processing Algorithms and API, W3C Candidate Recommendation, 2019-12-12 or newer + - JSON-LD 1.1 Framing, W3C Candidate Recommendation, 2019-12-12 or newer - [PyOBO](https://github.com/pyobo/pyobo) - docs: https://pyobo.readthedocs.io - features: From 7597bce752719dc3de9386f84efe9f5c10664551 Mon Sep 17 00:00:00 2001 From: Open Risk Date: Mon, 14 Feb 2022 16:31:19 +0100 Subject: [PATCH 06/28] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index dc03887..75cdc14 100644 --- a/README.md +++ b/README.md @@ -194,7 +194,7 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - docs: https://rdflib.readthedocs.io/ - graphical package overview: https://rdflib.dev/ - features: - - parsers and serializers for RDF/XML, NTriples, Turtle and more + - parsers and serializers for RDF/XML, NTriples, Turtle, JSON-LD and more - a graph interface which can be backed by any one of a number of store implementations - store implementations for in-memory storage and persistent storage - a SPARQL 1.1 implementation – supporting SPARQL 1.1 Queries and Update statements From 9f0c7c21d066c185cb71b27b8a29074887018426 Mon Sep 17 00:00:00 2001 From: Lorenzo Date: Wed, 16 Feb 2022 11:07:32 +0000 Subject: [PATCH 07/28] Add Hydra Ecosystem --- README.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/README.md b/README.md index 75cdc14..51f748b 100644 --- a/README.md +++ b/README.md @@ -236,6 +236,17 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - [ontology](https://github.com/ozekik/awesome-ontology) – A curated list of ontology things (with some python-related entries) - [awesome-semantic-web#python](https://github.com/semantalytics/awesome-semantic-web#python) Python section of awesome list for semantic-web-related projects - [github-semantic-web-python](https://github.com/topics/semantic-web?l=python) – github project search with `topic=semantic-web` and `language=python` +- [Hydra Ecosystem](https://github.com/HTTP-APIs) - Semantically Linked REST APIs + - docs: https://www.hydraecosystem.org/ + - tutorials: the stack has three major layers ([server](https://github.com/HTTP-APIs/hydrus), [client](https://github.com/HTTP-APIs/hydra-python-agent), [GUI](https://github.com/HTTP-APIs/hydra-python-agent-gui)); each repo has it own README + - features: + - deploy a server automatically from API Documentation (JSON-LD and W3C Hydra) + - client automatically reads the documentation and provides access to endpoints + - GUI allows visualization of the network generated by the servers and external resources + - a [parser](https://github.com/HTTP-APIs/hydra-openapi-parser) for OpenAPI specs translation + - notes: + - under development, experimental + - part of Google Summer of Code - [Pywikibot](https://github.com/wikimedia/pywikibot) - Library to interact with Wikidata and Wikimedia API - see also: https://www.wikidata.org/wiki/Wikidata:Creating_a_bot#Pywikibot From 0cf2ccce30809cf7f8b202125226f39405457b6f Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Thu, 17 Feb 2022 12:49:09 +0100 Subject: [PATCH 08/28] add ROBOT (for reasoner access) --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 51f748b..fba52e3 100644 --- a/README.md +++ b/README.md @@ -190,6 +190,10 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - publication: https://link.springer.com/chapter/10.1007%2F978-3-030-80418-3_11 - [Reasonable](https://github.com/gtfierro/reasonable) – An OWL 2 RL reasoner with reasonable performance - written in Rust with Python-Bindings (via [pyo3](https://pyo3.rs/)) +-[ROBOT](https://github.com/ontodev/robot) – Java-tool for automating ontology workflow with several reasoners (ELK, Hermite, ...) and Python interface + - General docs: https://robot.obolibrary.org/ + - Python interfaces: https://robot.obolibrary.org/python + - Docs on reasoning: https://robot.obolibrary.org/reason - [rdflib](https://github.com/RDFLib/rdflib) – Python package for working with RDF - docs: https://rdflib.readthedocs.io/ - graphical package overview: https://rdflib.dev/ From df99797ea13245db3ffd18918f90ec31348a3490 Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Fri, 18 Feb 2022 11:46:29 +0100 Subject: [PATCH 09/28] Delete subjective_notes.md --- subjective_notes.md | 55 --------------------------------------------- 1 file changed, 55 deletions(-) delete mode 100644 subjective_notes.md diff --git a/subjective_notes.md b/subjective_notes.md deleted file mode 100644 index b0bfd58..0000000 --- a/subjective_notes.md +++ /dev/null @@ -1,55 +0,0 @@ -# General Information - -This file serves to publicly note some subjective thoughts which currently do not have a better place to live. - - -# Possible Issues for other Projects: - -This section collects *observations* that I perceive as classical *issues* for a software project, i.e. things that could be improved. - -## Owlready - -- There should be an official issue tracker -- The code should be automatically checked by some continuous integration service - - Potential problems waste of energy and ressources through cloud services. - - Potential solution: configure CI such that only selected branches are tracked, like in [`.drone.yml` in yamlpyowl](https://github.com/cknoll/yamlpyowl/blob/main/.drone.yml). -- Change the extension handling in `setup.py`. Reason: The usage of `cython` in `setup.py` is [not recommended by the cython documentation](https://docs.cython.org/en/latest/src/userguide/source_files_and_compilation.html#distributing-cython-modules). -- Disable the "owlready2_optimized"-warning in `driver.py`. The user should be warned during installation but not on every use of the library. Also the doc says: "its use is entirely optional", thus a warning every time seems inappropriate. -- Change the representation of `owlready2.Thing` and its subclasses. Currently this reads like `repr(owl2.Thing)` → `< 'Thing'>`. However "object property" IMHO has a different meaning in the context of OWL, see e.g. [owl2-primer](https://www.w3.org/TR/owl2-primer/). -- Check if newer versions of Reasoners are available. At least Pellet seems to be outdated. -- Call JAVA-Reasoners directly instead of using `subprocess`. This might be relevant: -- Update docs to current version. - - Ideally, docs should be built automatically when a new version is released. - - Also, docs should be available for past versions too. -- [docs on custom rendering](https://owlready2.readthedocs.io/en/latest/annotations.html#custom-rendering-of-entities) should provide information how to restore the original behavior - - this can be done with `set_render_func(default_render_func)`, see also - - - -# 404 – A General Impression of the Semantic Web World - -Reproducibility and Comprehensibiltiy seems to be a core goal of the whole semantic web idea. However, I discovered a surprisingly high percentage of orphaned projects. An incomplete list (compiled since spring 2021): - -- http://www.semanticweb.org/ (time out) -- https://www.semanticdesktop.org/ - - links to: http://www.semanticweb.org/wiki/Semantic_Desktop (time out) -- https://www.w3.org/2001/sw/wiki/Neologism - - links to: http://neologism.deri.ie/ (time out) -- https://bioportal.bioontology.org/projects/TODE - - links to: http://ontologicaldiscovery.org/ (time out) - -- https://lod-cloud.net/dataset/msc - - links to: http://msc2010.org/mscwork/ - - links to: http://4store.org/trac/wiki/SparqlServer (404) - - links to: (404) - - https://lod-cloud.net/dataset/fu-berlin-eurostat - - https://lod-cloud.net/dataset/bfs-linked-data - - links to: mailto:project-msc-lod@jacobs-university.de (automatic response: unreachable) -- https://github.com/bfo-ontology/BFO/wiki - - links to: http://ifomis.uni-saarland.de/bfo/discussion (404) -- many of the [publicly listed wikibase instances](https://wikibase-registry-query.wmflabs.org/#%23defaultView%3ATimeline%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FcreationDate%20%28SAMPLE%28%3Flogo%29%20AS%20%3Fimage%29%0AWHERE%0A%7B%0A%20%20%20%20%3Fitem%20wdt%3AP11%20wd%3AQ20%20.%0A%20%20%20%20%3Fitem%20wdt%3AP5%20%3FcreationDate%20.%0A%09SERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%2Cen%22%20%7D%0A%20%20%20%20OPTIONAL%20%7B%20%3Fitem%20wdt%3AP8%20%3Flogo%20%7D%0A%7D%0AGROUP%20BY%20%3Fitem%20%3FitemLabel%20%3FcreationDate) (see also [here](https://wikibase-registry.wmflabs.org/wiki/Main_Page)) are not available (either 404 or 503 problems). -- https://www.isko.org/ko.html (International Society for Knowledge Organization) -> KOS registry -> https://bartoc.org/ - - https://bartoc.org/vocabularies?search=engineering - - "Sorry, we have some technical problems! Please contact the administrator and include the error message below." (no error message shown) -- https://en.wikipedia.org/wiki/UMBEL → http://umbel.org/ → Online Casinos in Australia -- http://www.visualdataweb.de/webvowl/ Operation stopped in Oct. 2021 From e90f6dfc19f6255a5e0cec1fe8cb49f3a8aa6759 Mon Sep 17 00:00:00 2001 From: Evgeny Blokhin Date: Fri, 18 Feb 2022 17:55:51 +0100 Subject: [PATCH 10/28] Add our ongoing work on the FaCT++ Python interface --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index fba52e3..8238b66 100644 --- a/README.md +++ b/README.md @@ -182,7 +182,6 @@ Furthermore, this repository might serve as a **cristallization point for a comm by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Marx in Journal of Web Semantics, 2018 [[@sciencedirect](https://www.sciencedirect.com/science/article/pii/S1570826818300416)] [[@arXiv](https://arxiv.org/abs/1805.03721)] - - [RaiseWikibase](https://github.com/UB-Mannheim/RaiseWikibase) – A tool for speeding up multilingual knowledge graph construction with Wikibase - fast inserts into a Wikibase instance: creates up to a million entities and wikitexts per hour - docs: https://ub-mannheim.github.io/RaiseWikibase/ @@ -190,7 +189,7 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - publication: https://link.springer.com/chapter/10.1007%2F978-3-030-80418-3_11 - [Reasonable](https://github.com/gtfierro/reasonable) – An OWL 2 RL reasoner with reasonable performance - written in Rust with Python-Bindings (via [pyo3](https://pyo3.rs/)) --[ROBOT](https://github.com/ontodev/robot) – Java-tool for automating ontology workflow with several reasoners (ELK, Hermite, ...) and Python interface +- [ROBOT](https://github.com/ontodev/robot) – Java-tool for automating ontology workflow with several reasoners (ELK, Hermite, ...) and Python interface - General docs: https://robot.obolibrary.org/ - Python interfaces: https://robot.obolibrary.org/python - Docs on reasoning: https://robot.obolibrary.org/reason @@ -202,7 +201,7 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - a graph interface which can be backed by any one of a number of store implementations - store implementations for in-memory storage and persistent storage - a SPARQL 1.1 implementation – supporting SPARQL 1.1 Queries and Update statements - + - FaCT++ OWL 2 reasoner integration: https://github.com/tilde-lab/pyfactxx (_work in progress_) - [SPARQL kernel](https://github.com/paulovn/sparql-kernel) for Jupyter - features: - sending queries to an SPARQL endpoint From 40147ef881f6755e252fea2dc28cba3f34b50482 Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Fri, 18 Feb 2022 23:09:51 +0100 Subject: [PATCH 11/28] Move pyfactxx entry; adapt styling --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 8238b66..69c9240 100644 --- a/README.md +++ b/README.md @@ -151,6 +151,11 @@ Furthermore, this repository might serve as a **cristallization point for a comm - features: -supports several ontology languages and formats - docs: https://pronto.readthedocs.io/en/latest/api.html +- [pyfactxx](https://github.com/tilde-lab/pyfactxx) – python bindings for FaCT++ OWL 2 (C++ reasoner) + - features: + - well-optimized reasoner for SROIQ(D) description logic + - notes: + - _work in progress_) - [PyFuseki](https://github.com/yubinCloud/pyfuseki) – Library that interact with Jena Fuseki (SPARQL server): - docs: https://yubincloud.github.io/pyfuseki/ - [PyLD](https://github.com/digitalbazaar/pyld) - A JSON-LD processor written in Python @@ -201,7 +206,6 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - a graph interface which can be backed by any one of a number of store implementations - store implementations for in-memory storage and persistent storage - a SPARQL 1.1 implementation – supporting SPARQL 1.1 Queries and Update statements - - FaCT++ OWL 2 reasoner integration: https://github.com/tilde-lab/pyfactxx (_work in progress_) - [SPARQL kernel](https://github.com/paulovn/sparql-kernel) for Jupyter - features: - sending queries to an SPARQL endpoint From 0bffa812af8542f1c414be85e69d818beba31955 Mon Sep 17 00:00:00 2001 From: Evgeny Blokhin Date: Sun, 20 Feb 2022 00:39:36 +0100 Subject: [PATCH 12/28] Update PR #17 --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 69c9240..2532a0d 100644 --- a/README.md +++ b/README.md @@ -151,11 +151,12 @@ Furthermore, this repository might serve as a **cristallization point for a comm - features: -supports several ontology languages and formats - docs: https://pronto.readthedocs.io/en/latest/api.html -- [pyfactxx](https://github.com/tilde-lab/pyfactxx) – python bindings for FaCT++ OWL 2 (C++ reasoner) +- [pyfactxx](https://github.com/tilde-lab/pyfactxx) – python bindings for FaCT++ OWL 2 C++ reasoner - features: - well-optimized reasoner for SROIQ(D) description logic + - [rdflib](https://github.com/RDFLib/rdflib) integration - notes: - - _work in progress_) + - _work in progress_ - [PyFuseki](https://github.com/yubinCloud/pyfuseki) – Library that interact with Jena Fuseki (SPARQL server): - docs: https://yubincloud.github.io/pyfuseki/ - [PyLD](https://github.com/digitalbazaar/pyld) - A JSON-LD processor written in Python From a358103329c4ec0a56312eb8674bbdcff59ba5a9 Mon Sep 17 00:00:00 2001 From: Timo Date: Mon, 21 Feb 2022 17:44:00 +0100 Subject: [PATCH 13/28] Added SPARQLing Unicorn QGIS Plugin reference --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index 2532a0d..cdc1816 100644 --- a/README.md +++ b/README.md @@ -211,6 +211,14 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - features: - sending queries to an SPARQL endpoint - fetching and presenting the results in a notebook +- [SPARQLing Unicorn QGIS Plugin](https://github.com/sparqlunicorn/sparqlunicornGoesGIS) + - docs: https://sparqlunicorn.github.io/sparqlunicornGoesGIS/ + - QGIS plugin page: https://plugins.qgis.org/plugins/sparqlunicorn/ + - features: + - Querying geospatial vector layers from SPARQL endpoints + - Conversion of geoformats (GeoJSON, SHP, KML, GML, etc.) to geospatial RDF + - Conversion of RDF geodata (GeoSPARQL-formatted) from one coordinate reference system to another + - SHACL validation of geospatial RDF graphs including validation of geoliteral (WKT, GML) contents - [WikidataIntegrator](https://github.com/SuLab/WikidataIntegrator) – Library for reading and writing to Wikidata/Wikibase - features: - high integration with the Wikidata SPARQL endpoint From 91b812f8d27bdc99a7c04a7e3907d867adde2fb8 Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Tue, 22 Feb 2022 10:06:47 +0100 Subject: [PATCH 14/28] Update entry: SPARQLing Unicorn QGIS Plugin --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index cdc1816..f311d1a 100644 --- a/README.md +++ b/README.md @@ -211,7 +211,7 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - features: - sending queries to an SPARQL endpoint - fetching and presenting the results in a notebook -- [SPARQLing Unicorn QGIS Plugin](https://github.com/sparqlunicorn/sparqlunicornGoesGIS) +- [SPARQLing Unicorn QGIS Plugin](https://github.com/sparqlunicorn/sparqlunicornGoesGIS) – QGIS plugin which adds a GeoJSON layer from SPARQL enpoint queries - docs: https://sparqlunicorn.github.io/sparqlunicornGoesGIS/ - QGIS plugin page: https://plugins.qgis.org/plugins/sparqlunicorn/ - features: From 2d7b134336b9c21dc84f0ea144c3440b3e5029f6 Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Tue, 22 Feb 2022 10:29:59 +0100 Subject: [PATCH 15/28] Add entry: pyLoDStorage --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index f311d1a..cf12007 100644 --- a/README.md +++ b/README.md @@ -164,6 +164,12 @@ Furthermore, this repository might serve as a **cristallization point for a comm - JSON-LD 1.1, W3C Candidate Recommendation, 2019-12-12 or newer - JSON-LD 1.1 Processing Algorithms and API, W3C Candidate Recommendation, 2019-12-12 or newer - JSON-LD 1.1 Framing, W3C Candidate Recommendation, 2019-12-12 or newer +- [pyLoDStorage](https://github.com/WolfgangFahl/pyLoDStorage) – python library to interchange data between SPARQL-, JSON and SQL-endpoints + - features: + - Integration of [tabulate library](https://pypi.org/project/tabulate/) + - QueryManager class for handling named queries + - Basic data structure: **l**ists of **d**icts (thus: "LoD") + - docs: https://wiki.bitplan.com/index.php/PyLoDStorage - [PyOBO](https://github.com/pyobo/pyobo) - docs: https://pyobo.readthedocs.io - features: From 934536cfacb8031bbb5b5c038f2e2c30038d63e7 Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Tue, 22 Feb 2022 12:57:01 +0100 Subject: [PATCH 16/28] add entry: SPARQLWrapper --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index cf12007..3bbe6b8 100644 --- a/README.md +++ b/README.md @@ -225,6 +225,11 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - Conversion of geoformats (GeoJSON, SHP, KML, GML, etc.) to geospatial RDF - Conversion of RDF geodata (GeoSPARQL-formatted) from one coordinate reference system to another - SHACL validation of geospatial RDF graphs including validation of geoliteral (WKT, GML) contents +- [SPARQLWrapper](https://github.com/RDFLib/sparqlwrapper) – A wrapper for a remote SPARQL endpoint + - docs: https://sparqlwrapper.readthedocs.io/en/latest/index.html + - features: + - Creating a query invocation + - Optionally converting the result into a more manageable format - [WikidataIntegrator](https://github.com/SuLab/WikidataIntegrator) – Library for reading and writing to Wikidata/Wikibase - features: - high integration with the Wikidata SPARQL endpoint From 2c16ddec29e1b8d2d8cc1fdde63e9837f4422c51 Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Sun, 10 Apr 2022 14:48:54 +0200 Subject: [PATCH 17/28] add links to serd (close #14) --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 3bbe6b8..2702242 100644 --- a/README.md +++ b/README.md @@ -213,6 +213,8 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - a graph interface which can be backed by any one of a number of store implementations - store implementations for in-memory storage and persistent storage - a SPARQL 1.1 implementation – supporting SPARQL 1.1 Queries and Update statements +- [serd](https://gitlab.com/drobilla/python-serd) – Python serd module, providing bindings for Serd, a lightweight C library for working with RDF data + - docs: https://drobilla.gitlab.io/python-serd/singlehtml/ - [SPARQL kernel](https://github.com/paulovn/sparql-kernel) for Jupyter - features: - sending queries to an SPARQL endpoint From 170282c37cbc7e8b4019aafa79afd30a3746708a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Juli=C3=A1n=20Arenas=20Guerrero?= <18464038+ArenasGuerreroJulian@users.noreply.github.com> Date: Wed, 20 Apr 2022 17:28:55 +0200 Subject: [PATCH 18/28] Update morph with support for RML-star and link to the new docs --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 2702242..97344cc 100644 --- a/README.md +++ b/README.md @@ -101,12 +101,12 @@ Furthermore, this repository might serve as a **cristallization point for a comm - Verifying (non-trivial) logical consistency of a CLIF ontology - Proving theorems/lemmas, such as properties of concepts and relations or competency questions - GUI (alpha state) -- [Morph-KGC](https://github.com/oeg-upm/morph-kgc) – Engine to create RDF knowledge graphs from heterogeneous sources with R2RML and RML - - docs: https://github.com/oeg-upm/Morph-KGC/wiki +- [Morph-KGC](https://github.com/oeg-upm/morph-kgc) – Engine to create RDF and RDF-star knowledge graphs from heterogeneous sources with R2RML, RML and RML-str + - docs: https://morph-kgc.readthedocs.io - features: - support for relational databases, tabular files (e.g. CSV, Excel, Parquet) and hierarchical files (XML and JSON) - - generates the RDF by running the engine through command line - - can be used as a library to load the RDF knowledge graph to RDFlib + - generates the RDF and RDF-star knowledge graphs by running through command line or as a library + - Integrates with RDFlib and Oxigraph to load the generated RDF directly to those libraries - [nxontology](https://github.com/related-sciences/nxontology) – NetworkX-based library for representing ontologies - features: - load ontologies into a `networkx.DiGraph` or `MultiDiGraph` from `.obo`, `.json`, or `.owl` formats From 45e4992235f4207ff88ba1d6e297efb5e2d0cd59 Mon Sep 17 00:00:00 2001 From: Vincent Emonet Date: Mon, 13 Jun 2022 15:28:51 +0200 Subject: [PATCH 19/28] add entry for rdflib-endpoint --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 97344cc..bdbdd42 100644 --- a/README.md +++ b/README.md @@ -213,6 +213,10 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - a graph interface which can be backed by any one of a number of store implementations - store implementations for in-memory storage and persistent storage - a SPARQL 1.1 implementation – supporting SPARQL 1.1 Queries and Update statements +- [rdflib-endpoint](https://github.com/vemonet/rdflib-endpoint) – Python package for easily deploying SPARQL endpoints for RDFLib Graphs + - features: + - exposing machine learning models or any other logic implemented in Python through a SPARQL endpoint, using custom functions + - serving local RDF files using the command line interface - [serd](https://gitlab.com/drobilla/python-serd) – Python serd module, providing bindings for Serd, a lightweight C library for working with RDF data - docs: https://drobilla.gitlab.io/python-serd/singlehtml/ - [SPARQL kernel](https://github.com/paulovn/sparql-kernel) for Jupyter From 5fbe79e06ab40bc139e586f922b4b1f358ef5e95 Mon Sep 17 00:00:00 2001 From: Nicolas Chauvat Date: Wed, 6 Jul 2022 12:25:12 +0200 Subject: [PATCH 20/28] add entry for CubicWeb --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index bdbdd42..67c5572 100644 --- a/README.md +++ b/README.md @@ -28,6 +28,16 @@ Furthermore, this repository might serve as a **cristallization point for a comm - Tutorial series on "how to pick tools and then use Python for using and manipulating the KBpedia knowledge graph" - [Material in form of Jupyter Notebooks](https://github.com/Cognonto/CWPK), - accompanying python package [cowpoke](https://github.com/Cognonto/cowpoke), +- [CubicWeb](https://www.cubicweb.org/) a framework to build semantic web applications + - website: https://www.cubicweb.org + - docs: https://cubicweb.readthedocs.io/en/latest/ + - features: + - An engine driven by the explicit data model of the application + - RQL, an intuitive query language close to the business vocabulary + - An architecture that separates data selection and visualisation + - Data security by design + - An efficient data storage + - [Eddy](https://github.com/obdasystems/eddy) - graphical ontology editor - website: https://www.obdasystems.com/eddy - features: From 70bf899e346247a6c0c99e9fec8ae3ace4b90d59 Mon Sep 17 00:00:00 2001 From: Evgeny Blokhin Date: Thu, 21 Jul 2022 01:30:15 +0200 Subject: [PATCH 21/28] Introduce completed pyfactxx: RDFlib <-> FaCT++ interface --- README.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 67c5572..5de7530 100644 --- a/README.md +++ b/README.md @@ -161,12 +161,11 @@ Furthermore, this repository might serve as a **cristallization point for a comm - features: -supports several ontology languages and formats - docs: https://pronto.readthedocs.io/en/latest/api.html -- [pyfactxx](https://github.com/tilde-lab/pyfactxx) – python bindings for FaCT++ OWL 2 C++ reasoner +- [pyfactxx](https://github.com/tilde-lab/pyfactxx) – Python bindings for FaCT++ OWL 2 C++ reasoner - features: - - well-optimized reasoner for SROIQ(D) description logic + - well-optimized reasoner for SROIQ(D) description logic, with additional improvements - [rdflib](https://github.com/RDFLib/rdflib) integration - - notes: - - _work in progress_ + - easy cross-platform installation - [PyFuseki](https://github.com/yubinCloud/pyfuseki) – Library that interact with Jena Fuseki (SPARQL server): - docs: https://yubincloud.github.io/pyfuseki/ - [PyLD](https://github.com/digitalbazaar/pyld) - A JSON-LD processor written in Python From b2558a13acfa75647488b001de828614efebb69f Mon Sep 17 00:00:00 2001 From: "C. Knoll" Date: Sun, 11 Sep 2022 13:08:27 +0200 Subject: [PATCH 22/28] =?UTF-8?q?add=20"Graph=20Thinking"=20=E2=80=93=20Ta?= =?UTF-8?q?lk=20by=20@ceteri?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 5de7530..d2a7675 100644 --- a/README.md +++ b/README.md @@ -278,6 +278,7 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - [ontology](https://github.com/ozekik/awesome-ontology) – A curated list of ontology things (with some python-related entries) - [awesome-semantic-web#python](https://github.com/semantalytics/awesome-semantic-web#python) Python section of awesome list for semantic-web-related projects - [github-semantic-web-python](https://github.com/topics/semantic-web?l=python) – github project search with `topic=semantic-web` and `language=python` +- "Graph Thinking" – Talk by Paco Nathan ([@ceteri](https://github.com/ceteri)) PyData Global 2021; [slides](https://derwen.ai/s/kcgh#84), [video](https://www.youtube.com/watch?v=bqku2a7ScXg) - [Hydra Ecosystem](https://github.com/HTTP-APIs) - Semantically Linked REST APIs - docs: https://www.hydraecosystem.org/ - tutorials: the stack has three major layers ([server](https://github.com/HTTP-APIs/hydrus), [client](https://github.com/HTTP-APIs/hydra-python-agent), [GUI](https://github.com/HTTP-APIs/hydra-python-agent-gui)); each repo has it own README From 350412ae475f7ed64afdcb504861fab4810fc1ce Mon Sep 17 00:00:00 2001 From: Felix Ocker Date: Wed, 21 Sep 2022 13:41:17 +0200 Subject: [PATCH 23/28] add entry for pystardog --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index d2a7675..a40a55b 100644 --- a/README.md +++ b/README.md @@ -194,6 +194,8 @@ Furthermore, this repository might serve as a **cristallization point for a comm - resolution-based theorem provers for first-order logic - focus on good comprehensibility of the code - Literature: [Teaching Automated Theorem Proving by Example](https://link.springer.com/chapter/10.1007/978-3-030-51054-1_9) +- [pystardog](https://github.com/stardog-union/pystardog) + - Python bindings for the [Stardog Knowledge Graph platform](https://www.stardog.com/) - [Quit Store](https://github.com/AKSW/QuitStore) – workspace for distributed collaborative Linked Data knowledge engineering ("Quads in Git") - features: - read and write RDF Datasets From b7af9ecb794180eb062203754b82a5dd8e9bdeed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Juli=C3=A1n=20Arenas=20Guerrero?= <18464038+ArenasGuerreroJulian@users.noreply.github.com> Date: Sun, 20 Nov 2022 13:51:32 +0100 Subject: [PATCH 24/28] Update morph-kgc --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a40a55b..b1c33ce 100644 --- a/README.md +++ b/README.md @@ -111,12 +111,12 @@ Furthermore, this repository might serve as a **cristallization point for a comm - Verifying (non-trivial) logical consistency of a CLIF ontology - Proving theorems/lemmas, such as properties of concepts and relations or competency questions - GUI (alpha state) -- [Morph-KGC](https://github.com/oeg-upm/morph-kgc) – Engine to create RDF and RDF-star knowledge graphs from heterogeneous sources with R2RML, RML and RML-str +- [Morph-KGC](https://github.com/oeg-upm/morph-kgc) – System to create RDF and RDF-star knowledge graphs from heterogeneous sources with R2RML, RML and RML-star - docs: https://morph-kgc.readthedocs.io - features: - support for relational databases, tabular files (e.g. CSV, Excel, Parquet) and hierarchical files (XML and JSON) - - generates the RDF and RDF-star knowledge graphs by running through command line or as a library - - Integrates with RDFlib and Oxigraph to load the generated RDF directly to those libraries + - generates RDF and RDF-star knowledge graphs by running through the command line or as a library + - integrates with RDFlib and Oxigraph to load the generated RDF directly to those libraries - [nxontology](https://github.com/related-sciences/nxontology) – NetworkX-based library for representing ontologies - features: - load ontologies into a `networkx.DiGraph` or `MultiDiGraph` from `.obo`, `.json`, or `.owl` formats From 74121c959cae23cabb1f1b584953ec3790b30b22 Mon Sep 17 00:00:00 2001 From: Carsten Knoll Date: Sat, 8 Jul 2023 14:46:49 +0200 Subject: [PATCH 25/28] add sparqlfun (SPARQL template library by @cmungall) to overview doc --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index b1c33ce..b0a7db3 100644 --- a/README.md +++ b/README.md @@ -230,6 +230,16 @@ by Natanael Arndt, Patrick Naumann, Norman Radtke, Michael Martin, and Edgard Ma - serving local RDF files using the command line interface - [serd](https://gitlab.com/drobilla/python-serd) – Python serd module, providing bindings for Serd, a lightweight C library for working with RDF data - docs: https://drobilla.gitlab.io/python-serd/singlehtml/ +- [ sparqlfun](https://github.com/linkml/sparqlfun) + - LinkML based SPARQL template library and execution engine + - modularized core library of SPARQL templates + - Fully FAIR description of templates + - Rich expressive language for moedeling templates + - uses [LinkML](https://linkml.io/linkml/) as base language + - optional python bindings / [object model](https://github.com/linkml/sparqlfun/blob/main/sparqlfun/model.py) using LinkML + - supports both SELECT and CONSTRUCT + - optional export to TSV, JSON, YAML, RDF + - extensive [endpoint metadata](https://github.com/linkml/sparqlfun/tree/main/sparqlfun/config) - [SPARQL kernel](https://github.com/paulovn/sparql-kernel) for Jupyter - features: - sending queries to an SPARQL endpoint From 8497760bd637441353133a44538b5546fd3e9380 Mon Sep 17 00:00:00 2001 From: Carsten Knoll Date: Sat, 8 Jul 2023 14:59:26 +0200 Subject: [PATCH 26/28] add PyKEEN (Python KnowlEdge EmbeddiNgs to overview --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index b0a7db3..2e8d458 100644 --- a/README.md +++ b/README.md @@ -168,6 +168,13 @@ Furthermore, this repository might serve as a **cristallization point for a comm - easy cross-platform installation - [PyFuseki](https://github.com/yubinCloud/pyfuseki) – Library that interact with Jena Fuseki (SPARQL server): - docs: https://yubincloud.github.io/pyfuseki/ + +- [PyKEEN](https://github.com/pykeen/pykeen) (**Py**thon **K**nowl**E**dge **E**mbeddi**N**gs) – Python package to train and evaluate knowledge graph embedding models + - features: + - 44 Models + - 37 Datasets + - 5 Inductive Datasets + - support for multi-modal information - [PyLD](https://github.com/digitalbazaar/pyld) - A JSON-LD processor written in Python - conforms: - JSON-LD 1.1, W3C Candidate Recommendation, 2019-12-12 or newer From 0f5069099504f4c6f6d73ed83487f5ba218ad5ac Mon Sep 17 00:00:00 2001 From: Felix Ocker Date: Thu, 26 Oct 2023 22:48:28 +0200 Subject: [PATCH 27/28] add LangChain's GraphSparqlQAChain --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index 2e8d458..7a56f50 100644 --- a/README.md +++ b/README.md @@ -99,6 +99,12 @@ Furthermore, this repository might serve as a **cristallization point for a comm - OWL - OBOGraph JSON format - SSSOM +- [LangChain](https://github.com/langchain-ai/langchain)'s GraphSparqlQAChain – A LangChain module for making RDF and OWL accessible via natural language + - docs: https://python.langchain.com/docs/use_cases/graph/graph_sparql_qa + - features: + - Generates SPARQL SELECT and UPDATE queries from natural language + - Runs the generated queries against local files, endpoints, or triple stores + - Returns natural language responses - [LinkML](https://github.com/linkml/linkml) – Linked Open Data Modeling Language - features: - A high level simple way of specifying data models, optionally enhanced with semantic annotations From f699d97eeead6aad4d6ca6899d5bf9e1f5a26e74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Juli=C3=A1n=20Arenas=20Guerrero?= <18464038+arenas-guerrero-julian@users.noreply.github.com> Date: Mon, 19 May 2025 18:43:32 +0200 Subject: [PATCH 28/28] Add pycottas --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index 7a56f50..1f49019 100644 --- a/README.md +++ b/README.md @@ -167,6 +167,12 @@ Furthermore, this repository might serve as a **cristallization point for a comm - features: -supports several ontology languages and formats - docs: https://pronto.readthedocs.io/en/latest/api.html +- [pycottas](https://github.com/arenas-guerrero-julian/pycottas) – Library for working with compressed COTTAS files + - docs: https://pycottas.readthedocs.io + - features: + - compress RDF files to COTTAS format + - evaluate triple patterns over compressed RDF + - integrates with RDFlib as a store backend to query COTTAS files with SPARQL - [pyfactxx](https://github.com/tilde-lab/pyfactxx) – Python bindings for FaCT++ OWL 2 C++ reasoner - features: - well-optimized reasoner for SROIQ(D) description logic, with additional improvements