ENQUIRE networks as graph databases and further improvements.

[Muszeb]

We summarize the improvements of this major release below:

• Fixed several vulnerabilities and error-catching logic at all levels of the source code.
• Updated Reactome pathway data and gene alias dictionary.
• Implemented retrieval of bibliographic metadata (authors, journal, DOI, etc...). This data is paired to PMIDs in the files
  .../tag...Complete_edges_literature_links.tsv and tmp-tag/efetch_inputs/CitationToPMID_record.tsv.
• The PecanPy package has been containerized and node2vec+ has been added and set as the default network embedding method in context_aware_gene_sets.R
  (previous behavior can be reproduced by setting -o invlogweight).
• Neo4j 2025.04.0 has been containerized and a new utility function ENQUIRE2KG.sh has been implemented to transform any newly created ENQUIRE network into a graph database of gene, MeSH, and PMID entities, allowing for cutting-edge querying approaches and further developments. We demonstrated its use by contextualizing in literature novel experimental results in this publication. The Docker repository remains unchanged, while the latest SIF image and ENQUIRE2KG.sh for Apptainer/Singularity have been deposited under a new DOI.
• New logo.

to the README

The new ENQUIRE logo.

Full Changelog: v3.0.1...v4.0.0

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