Frequently Asked Questions (FAQ)

My initial data changed

As we try to achieve the best possible data quality in an automatic manner, we implemented multiple standardization, sanitization, and canonicalization steps. If you are certain your initial data is of higher quality, please feel free to go directly to the Wikidata import step.

Flowchart

Your flowchart looks very nice! How did you draw it?

yarn global add @mermaid-js/mermaid-cli

mmdc -i docs/flowchart.mmd -o img/flowchart.svg

See https://github.com/mermaid-js/mermaid-cli for more info

Molconvert issue

At the moment, we use molconvert (commercial) for the structure to chemical name conversion. Since we cannot disseminate it, you won't be able to proceed to the translation except if you modify the following variables in src/paths.R accordingly:

works_locally_only <- TRUE // FALSE
molconvertPath <- adapt_path_to // "~/../../Applications/MarvinSuite/bin/molconvert"

PMID translation

If you want to be able to use the PMID translation with fewer limitations and it to work faster, you have to set an API key as described in the following vignette.