semanticchemistry
global-chem
| semanticchemistry | global-chem | |
|---|---|---|
| 1 | 51 | |
| 15 | 141 | |
| - | 1.4% | |
| 5.3 | 7.7 | |
| about 1 month ago | 6 days ago | |
| Java | Jupyter Notebook | |
| Creative Commons Zero v1.0 Universal | Mozilla Public License 2.0 |
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semanticchemistry
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Global-Chem: A Free Dictionary from Common Chemical Names to Molecules
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
global-chem
- Open Source Government for Transparent Chemical Data
- Standardizing Mechanisms for Organic Chemistry Reactions
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Learning Resources
You can learn from me if you want. I am teaching beginner to advanced material. I am also pouring some ideas into this project: https://www.globalchemistry.org/
- Alternative Jet Fuels
- Found in a book about chemical warfare agents... I don't think I've ever seen a 5-skull warning before!
- The ~120 Chemicals in Interstellar Space
- Running Python Script Online
- The ~400 Chemicals Inside Marijuana
- Writing Novichok and Other Nerve Agents in Russian to Molecules
What are some alternatives?
pathways2GO - Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
coveragepy - The code coverage tool for Python
PubChemPy - Python wrapper for the PubChem PUG REST API.
codecov-example
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.
ChickenTicket - Pure Python implementation of a cryptocurrency blockchain
Protégé - Protege Desktop
pywebcanvas
Faith
pygraphblas - GraphBLAS for Python
exercise_app
d3 - Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada: