Toxicology data: tools not mentioned in in text

[bedroesb]

Page: Toxicology data

In pull request #1249, we are implementing changes to how we handle tools, resulting in different rules for rendering the tools table at the bottom of pages. Going forward, only tools referenced in the text will be included in the bottom table of the page. Some of the tools have been tagged with the page_id of this page, and we are currently exploring how to incorporate these tools into the text.

Tools that are not mentioned in the text:

• [x] CAS Registry - The CAS Registry (Chemical Abstracts Service Registry) includes more than 188 million unique chemicals. CAS Registry Numbers are broadly used as a unique identifier for chemical substances. The Registry is maintained by CAS, a subdivision of the American Chemical Society.
• [x] EDKB - Endocrine Disruptor Knowledge Base is a platform designed to foster the development of computational predictive toxicology. This platform allows direct access to ten libraries containing the following resources: a biological activity database, QSAR training sets, in vitro and in vivo experimental data for more than 3,000 chemicals, literature citations, chemical-structure search capabilities.
• [x] EudraVigilance - The European database of suspected adverse drug reaction reports is a public resource aimed to provide access to reported suspected side-effects of drugs. Side-effects are defined according to the MedDRA ontology.
• [x] GHS Classification - GHS (Globally Harmonized System of Classification and Labelling of Chemicals) classification was developed by the United Nations in an attempt to align standards and chemical regulations in different countries. GHS includes criteria for the classification of health, physical and environmental hazards, and what information should be included on labels of hazardous chemicals and safety data sheets.
• [x] NBP - The National Biomonitoring Program (NBP) is a public resource that offers an assessment of nutritional status and the exposure of the U.S. population to environmental chemicals and toxic substances.
• [x] NPDS - The National Poison Data System (NPDS) is a resource that provides poisson exposure occurring in the US and some freely associated states.
• [x] Pharos - Pharos provides hazard, use, and exposure information on 140,872 chemicals and 180 different kinds of building products.
• [x] REACH registered substances - Portal with public data submitted to ECHA in REACH registration dossiers by substance manufacturers, importers, or their representatives, as laid out by the REACH Regulation (see Understanding REACH regulation).
• [x] RxNorm - RxNorm is a normalized naming system for medications that is maintained by the National Library of Medicine. Rxnorm provides unique identifiers and allows unambiguous communication of drug-related information across the American health computer systems.
• [x] T3DB - The Toxin and Toxin Target Database is a bioinformatics resource that combines exhaustive toxin data with toxin target information. Currently it presents more than 42,000 toxin-target associations extracted from other databases, government documents, books and scientific literature. Each toxin record includes data on chemical properties and descriptors, toxicity values and medical information.
• [x] Tox21_Toolbox - The Toxicology in the 21st Century program, or Tox21, is a unique collaboration between several federal agencies to develop new ways to rapidly test whether substances adversely affect human health. The Tox21 Toolbox contains data-analysis tools for accessing and visualizing Tox21 quantitative high-throughput screening (qHTS) 10K library data, as well as integrating with other publicly available data.
• TOXNET - The Toxicology Data Network (TOXNET) was a portal that allowed access to several relevant sources in the toxicological field. Nowadays, these sources have been integrated into other NLM resources.
• [x] TXG-MAPr - A tool that contains weighted gene co-expression networks obtained from the Primary Human Hepatocytes, rat kidney, and liver TG-GATEs dataset.

Would you kindly review these tools and determine if they should be mentioned (as a link) in the text? If necessary, please propose changes to the text through a pull request on this temporary instance of the RDMkit by clicking on the pencil icon next to the title and following the instructions in this guide. @manuelpastor, @jpinero, @palilsonjmr, @mmayerp, @lauportell

[bedroesb]

We will move to the new system in the week of the 24th of Juli, so please make sure changes are comments are made before this date. Thanks a lot in advance!

[jpinero]

The tools look good to me. I think they should be included. But I see no pencil on the temporary instance linked to the url. I see this

[martin-nc]

@jpinero I think @bedroesb is on holiday, but I think he means the Toxicology page on the temporary instance: https://bedroesb.github.io/rdmkit/toxicology_data

[bedroesb]

@martin-nc and @jpinero correct!

[lauportell]

Hi @jpinero do you have any update on how this is progressing? We would like to move soon to the new system and the tools are not yet in the text, if I see it correctly. Thank you!

[lauportell]

Hi @jpinero, As we didn't want all these tools to be lost, I tried to add them in the text. Can you please have a look and let me know if you think I did it correctly? The only tools I didn't place is 'TOXNET' that I would remove as it looks obsolete. Thank you. Laura.

[bedroesb]

Any feedback @manuelpastor, @jpinero, @palilsonjmr, @mmayerp on the updated page? : https://bedroesb.github.io/rdmkit/toxicology_data

[bedroesb]

We will move to the new system soon, so I will close this issue.