Skip to content

Reference for Parameters in NetMedEx

Source (web app only)

  • PubTator3 API: Search articles and generate networks from biological annotations in the collected articles

  • PubTator File: Generate networks from the annotation file (PubTator File), available via the PubTator button (see Search Articles and Generate Networks).

Search Type

CLI: netmedex search

  • Text Search (-q, --query): Use keywords to retrieve relevant articles

    • Examples:
      • "COVID 19" AND "PON1"
      • "liver cancer" AND "sorafenib"
    • Note: Use double quotes to match whole words and AND/OR to combine keywords.

  • PMID (-p, --pmids): Retrieve articles by PubMed Identifier (PMID)

    • Examples: 26578185,26952367
    • Note: Separate PMIDs by commas.

  • PMID File (-f, --pmid_file): Retrieve articles by a text file of PMIDs

    • Note: One PMID per line

Sort

CLI: netmedex search

  • Relevance (--sort score): Sort articles in descending order by relevance score (see how search results are prioritized in the PubTator3 Paper)

  • Recency (--sort date): Sort articles in descending order by publication date

This parameter affects the retrieved articles if the total number exceeds Max Articles.

PubTator3 Parameters

CLI: netmedex search

  • Use MeSH Vocabulary (--mesh): If enabled, standardize the text in the original content using MeSH vocabulary. If disabled, the text is lowercased and standardized using plural stemming.

  • Full Text (--full_text): If enabled, retrieve full-text annotations if available. If disabled, collect annotations from abstracts only.

    • For articles where only abstracts are available, annotations will be collected from the abstracts. As a result, the network may be generated from a mix of full-text articles and abstracts if this parameter is enabled.

Max Articles

CLI: netmedex search

  • Max Articles (--max_articles): Specify the maximum number of articles to retrieve.
    • This parameter applies to Text Search only. If search results exceed MAX_ARTICLES, only the top MAX_ARTICLES will be retrieved after sorting.

Node Filter (Node Type)

CLI: netmedex network

  • All (--node_type all): Retain all annotations (biological concepts with or without standardized MeSH terms).

  • MeSH (--node_type mesh): Retain annotations with standardized MeSH terms only.

  • BioREx Relation (--node_type relation): Retain only the annotations with high-confidence relationships as predicted by the BioREx model used in PubTator3. This results in a network that is not co-mention-based.

Weighting Method

CLI: netmedex network

  • Frequency (--weighting_method freq): Calculate edge weights using co-occurrence counts.

  • NPMI (--weighting_method npmi): Calculate edge weights using normalized pointwise mutual information (NPMI).

    • Edges will be assigned high weights if the concepts co-occur frequently. For exmaple, biological concepts that co-occur in only a few articles can still have a high edge weight if they almost always co-occur whenever each concept appears in an article.
    • The calculated NPMI ranges from -1 to 1. The weight is set to 0 for negative values.
    • This option is still experimental and requires further optimization.

Edge Weight Cutoff

CLI: netmedex network

  • Edge Weight Cutoff (--cut_weight INT): Set the minimum edge weight to filter the graph.
    • Raw edge weights (calculated using Frequency or NPMI) are scaled linearly between 0 and 20.
    • If set to 0, all edges are included.

See also Max Edges, which directly limits the number of edges.

Max Edges

  • Max Edges (--max_edges INT): Set the maximum number of edges in the graph.
    • After sorting edges by weight, only the top MAX_EDGES are retained. Isolated nodes are removed.
    • If set to 0, all edges are included.

Network Parameters

  • Community (--community): Group nodes into communities by the Louvain algorithm.

    • In essence, the Louvain algorithm groups nodes into communities that maximize intra-community links and minimize inter-community links.
    • This option is useful for visualizing dense networks.
    • Edges between nodes in separate communities are collapsed into a single community edge.
    • If enabled, the generated network currently cannot be exported in XGMML format.

  • --pmid_weight PMID_WEIGHT_FILE (CLI only): Path to the CSV file for the article weights.

Example CSV file (pmid_weight.csv):

26578185,1
26952367,2

Network Output Format

  • HTML (--format html): Export the network in HTML format.

  • XGMML (--format xgmml): Export the network in a Cytoscape-compatible format.

    • This generated file can be opened in Cytoscape for further analysis.

  • --format json (CLI only): Export the network info in JSON format.

Network Visualization Tools (web app only)

  • Graph Layout: Adjust the graph layout.

  • Edge Weight Cutoff: Dynamically adjust edge weight cutoff without resubmitting inputs. (See Edge Weight Cutoff)

  • Minimum Node Degree: Set the minimum node degree to filter the graph.

    • This option is useful for identifying hubs and their connections.