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. Not writing the text correctly may cause an operation to fail. For example, if you are using a pandas DataFrame and do not specify the concept type correctly, the resulting chart will be empty.
The concept types should be written exactly this way, including capitalization:
"Anatomy & Physiology" "Cell Biology" "Chemicals & Drugs" "Context" "Genetics" "Medical Conditions" "Medical Devices" "Medical Procedures" "Species & Viruses"
["concept_type"]=="Chemicals & Drugs"
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 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 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.
- Examples: Nurses, Libraries, National Cancer Institute, year, percent
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 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 refers to medical devices, instruments, and tools used in the care of patients.
- Examples: Arm Prostheses, Dentures, Needles, X-Ray
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 Viruses refers to taxonomies of organisms and viruses.
- Examples: Homo sapiens, Drosophila melanogaster, Escherichia coli, SARS, West Nile virus
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