integrated Dietary Supplements Knowledge Base (iDISK)

This readme.txt file was generated on 2019-11-21

Title of Dataset
Integrated Dietary Supplement Knowledge Base (iDISK)

Author Information
Rizvi, Rubina F
Vasilakes, Jake A
Adam, Terrence J
Melton, Genevieve B
Bishop, Jeffrey R
Bian, Jiang
Tao, Cui
Zhang, Rui (zhan1386@umn.edu)

University of Minnesota Institute for Health Informatics, Natural Language Processing / Information Extraction (NLP/IE) Program

Funding information:
This research was supported by National Center for Complementary and Integrative Health Award (#R01AT009457) (Zhang) and the Agency for Healthcare Research and Quality grant (#1R01HS022085) (Melton).

SHARING/ACCESS INFORMATION

License:

CC-By-SA Attribution-ShareAlike 3.0 United States

Recommended citation for the data:

    Rizvi, Rubina F; Vasilakes, Jake A; Adam, Terrence J; Melton, Genevieve B; Bishop, Jeffrey R; Bian, Jiang; Tao, Cui; Zhang, Rui. (2019). Integrated Dietary Supplement Knowledge Base (iDISK). Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/d6bm3v. 

** Description **
The integrated Dietary Supplements Knowledge Base (iDISK) covers a variety of
dietary supplements, including vitamins, herbs, minerals, etc. It was standardized
and integrated from the Dietary Supplements Label Database (DSLD), the “About Herbs”
database from Memorial Sloan Kettering Cancer Center (MSKCC), the Canadian Natural Health
Products and Ingredients database (NHP), and the Natural Medicines Comprehensive Database
(NMCD) developed by the Therapeutic Research Center (TRC). iDISK contains a variety of
attributes and relationships describing information about each dietary supplement such as
which products it is an ingredient of and what drugs it might interact with.
iDISK is available as a Neo4j graph database as well as UMLS style RRF files.
See the README for details on installing and using iDISK.
The code used to build iDISK is publicly available at https://github.com/jvasilakes/idisk.

NMCD is a commercial database and we have obtained special permission to use and redistribute the data publicly.

General Schema

iDISK contains 7 concept types and 6 relation types:

Concept Types

• SDSI: Semantic Dietary Supplement Ingredient
• DSP: Dietary Supplement Product
• DIS: Disease or Syndrome
• SPD: Pharmaceutical Drug
• SOC: System Organ Class
• SS: Sign or Symptom
• TC: Therapeutic Class

Following the UMLS, concepts are collections of synonymous atoms. An atom is a term
(e.g. a possible name for a supplement, such as “Ginkgo” or “Ginkgo Biloba”) from a
given data source.

Relation types

• has_adverse_effect_on(SDSI, SOC)
• has_adverse_reaction(SDSI, SS)
• has_ingredient(DSP, SDSI)
• has_therapeutic_class(SDSI, TC)
• interacts_with(SDSI, SPD)
• is_effective_for(SDSI, DIS)

Neo4j Release

The Neo4j release idisk-neo4j-<version>.dump can be loaded into an existing Neo4j graph using
the command

bin/neo4j-admin load --from=/path/to/idisk_neo4j-<version>.dump --database=<database>

This is most easily done from the “Terminal” tab in the Neo4j Desktop.

RRF Release

The RRF release idisk-rrf-<version>.zip borrows heavily from format of the UMLS Metathesaurus. There are four files:

• MRSTY.RRF: The types of each concept.
• MRCONSO.RRF: The atoms of each concept.
• MRSAT.RRF: The attributes of each concept or relationship (if applicable).
• MRREL.RRF: The relationships between concepts.

The RRF format is a flat-file pipe-delimited format similar to CSV.
A description of the fields of each file follows:

MRSTY.RRF

• CUI: The unique concept identifier.
• STY: The concept type.

MRCONSO.RRF

• CUI: The unique concept identifier.
• AUI: The unique atom identifier.
• STR: This atom’s string representation.
• TTY: Term type of this atom. CN: common name, SN: scientific name, SY: synonym (unspecified).
• SAB: Source database from where this atom was obtained.
• SCODE: The ID in the source (if available) of this atom.
• ISPREF: Y if this atom is the preferred term in the source, N otherwise.

MRSAT.RRF

• ATUI: The unique attribute identifier.
• UI: The unique concept or relationship identifier.
• STYPE: DSCUI if UI is a concept or DSRUI if UI is a relationship.
• ATN: The attribute name.
• ATV: The attribute value.
• SAB: Source database from where this attribute was obtained.

MRREL.RRF

• RUI: The unique relationship identifier.
• CUI1: The CUI of the subject concept of this relationship.
• REL: The relation type.
• CUI2: The CUI of the object concept of this relationship.
• SAB: Source database from where this relationship was obtained.