Concept Types

ScienceIO's concept types (concept_type) are broad categories to which specific biomedical concepts are assigned. These help to create high-level views of the data.

For example, you can group the data by concept type and see the top "Chemicals & Drugs" or "Medical Conditions." Note that while concept_type is useful for identifying broad concepts within records, the concept_id will inform you of the specific biomedical concepts are mentioned within your records.

Using Concept Types in Your Code

Make sure, if you wish to specify a concept type (like to filter results, for example), that you write it correctly in your code. The concept types should be written exactly this way, including capitalization:

"Context"
"Anatomy & Physiology"
"Cell Biology"
"Chemicals & Drugs"
"Context"
"Medical Devices"
"Medical Conditions"
"Genetics"
"Number"
"Medical Procedures"
"Species & Viruses"

For example:

["concept_type"]=="Chemicals & Drugs"

Not writing the text correctly may cause an operation to fail. If you are using a pandas DataFrame and do not specify the concept type correctly, the resulting chart will be empty.

Anatomy & Physiology

Anatomy & Physiology refers to the structure and function of and phenomena related to living things. This category includes organs, tissues, and physiological functions.

Examples: Kidney, Iliac Artery, Digestion, Prognosis, Immune response

Cell Biology

Cell Biology refers to cell types, cell components & organelles, and cell lines.

Examples: Nucleus, lysosomes, malignant tumor cells, muscle cells, HeLa cells, THP-1 cell

Chemicals & Drugs

Chemicals & Drugs refers to small molecules and certain proteins, such as therapeutic peptides, antibodies, and antigens.

Examples: DAPI, osimertinib, amino acids, platinum oxide, Von Willebrand antigen

Context

Context refers to concepts that provide broader context for other concepts in the same document such as references to groups, organizations, demographics, geographies, locations, date ranges, etc. Note: these labels are most likely to be re-assigned or refined in future updates.

Examples: Nurses, Libraries, National Cancer Institute, year, percent

Genetics

Genetics refers to a broad category of genetic concepts, including individual genes, gene products, nucleic acids, and specific mutations with RSIDs.

Examples: beta-actin, EGFR, p53, VEGF, Immunoglobulin E, rs3743930

Medical Conditions

Medical Conditions refers to diagnoses, infections, malignancies, maladies, and broad medical conditions that can inform patient care but are not diseases per se.

Examples: Abscess, Breast Cancer, Cachexia, High-Risk Pregnancy, Long QT Syndrome

Medical Devices

Medical Devices refers to medical devices, instruments, and tools used in the care of patients.

Examples: Arm Prostheses, Dentures, Needles, X-Ray

Medical Procedures

Medical Procedures refers to medical procedures (such as analytical, diagnostic, and therapeutic techniques), equipment, and interventions.

Examples: Blood Culture, CT PET Scan, Endoscopy, High-Protein Diet, Intradermal Injection

Species & Viruses

Species and Virus refers to taxonomies of organisms and viruses. Note: this will change to "Taxonomy" in a future version of the API.

Examples: Homo sapiens, Drosophila melanogaster, Escherichia coli, SARS, West Nile virus