pathways2GO VS semanticchemistry

Compare pathways2GO vs semanticchemistry and see what are their differences.

pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM) (by geneontology)
ontology geneontology pathways go-cam biopax
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semanticchemistry

Chemical Information Ontology (by semanticchemistry)
Chemistry ontology cheminformatics chemical-information obofoundry
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journals.plos.org
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pathways2GO semanticchemistry
1 1
8 15
- -
5.9 1.8
2 months ago 29 days ago
Java Java
- Creative Commons Zero v1.0 Universal
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pathways2GO

Posts with mentions or reviews of pathways2GO. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-08-04.

semanticchemistry

Posts with mentions or reviews of semanticchemistry. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-09-18.
  • Global-Chem: A Free Dictionary from Common Chemical Names to Molecules
    5 projects | news.ycombinator.com | 18 Sep 2022
    TIL about #cheminformatics and Linked Data (Semantic Web):

    Cheminformatics: https://en.wikipedia.org/wiki/Cheminformatics

    https://github.com/topics/cheminformatics :

    - https://github.com/hsiaoyi0504/awesome-cheminformatics #Databases #See_also

    - https://github.com/mcs07/PubChemPy :

    > PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.

    http://chemicalsemantics.com/introduction-to-the-chemical-se... ... /? chemicalsemantics github ... https://github.com/semanticchemistry/semanticchemistry #See_also :

    > The Chemical Information Ontology (CHEMINF) aims to establish a standard in representing chemical information. In particular, it aims to produce an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic or computed.

    Looks like they developed the CHEMINF OWL ontology in Protege 4 (which is Open Source). /ontology/cheminf-core.owl: https://github.com/semanticchemistry/semanticchemistry/blob/...

    - Does it -- the {sql/xml/json/graphql, RDFS Vocabulary, OWL Ontology} schema - have more (C)Classes and (P)Properties than other schema for modeling this domain?

    - What namespaced strings and URIs does it specify for linking entities internally and externally?

    LOV Linked Open Vocabularies maintains a database of many RDFS vocabularies and OWL ontologies (which are represented in RDF) https://lov.linkeddata.es/dataset/lov/terms?q=chemical

    - "The Linking Open Data Cloud" (2007-) https://lod-cloud.net/

    /? "cheminf" https://scholar.google.com/scholar?hl=en&as_sdt=0,43&qsp=1&q...

    /? "cheminf" ontology

What are some alternatives?

When comparing pathways2GO and semanticchemistry you can also consider the following projects:

Ontospy - Python library and command-line interface for inspecting and visualizing RDF models aka ontologies.

PubChemPy - Python wrapper for the PubChem PUG REST API.

ontology - Official Go implementation of the Ontology protocol. https://dev-docs.ont.io/#/

Widoco - Wizard for documenting ontologies. WIDOCO is a step by step generator of HTML templates with the documentation of your ontology. It uses the LODE environment to create part of the template.

Protégé - Protege Desktop

pathways2GO vs Ontospy semanticchemistry vs PubChemPy pathways2GO vs ontology semanticchemistry vs Widoco pathways2GO vs Widoco semanticchemistry vs Protégé pathways2GO vs Protégé