HemOnc vocabulary concepts
This page has short descriptions and examples of the concepts that have been parsed into the HemOnc ontology. Note that this is NOT the full HemOnc chemotherapy regimen model, as there are still concepts that are in the process of being defined and parsed. For information about how to obtain a copy of the ontology please go to this page.
- 1 Condition-level concepts
- 2 Protocol-level concepts
- 3 Regimen-level concepts
- 4 Component-level concepts
- 5 Study-level concepts
- 6 Publication-level concepts
- 7 Author-level concepts
- 8 Generic concepts
In the HemOnc vocabulary, a condition is the granular level at which treatments have been evaluated. For example, Colon cancer and Rectal cancer are conditions, whereas Colorectal cancer is a Condition Class.
- Examples: acquired coagulopathy, acute myeloid leukemia, adrenocortical carcinoma
Condition classes are containers for a subset of conditions. Most of these are organized by anatomy or disease category.
- Examples: classical hematologic condition, leukemia, malignant solid neoplasm
Context refers to the disease setting in which a treatment is administered. There are currently 33 contexts described in the HemOnc vocabulary, organized into a hierarchical structure with is a relationships.
- Examples: adjuvant therapy, non-curative first-line induction therapy, upfront therapy
- Example of relationships: adjuvant therapy is a post-definitive therapy is an upfront therapy is a curative therapy is an all lines of therapy
A protocol is the ordered combination of one or more Regimens. We are in the process of introducing this concept into the vocabulary - stay tuned!
Cycle Sigs (new in version 2020-01-25)
The timing of regimen cycles is captured as separate and distinct from the individual drug SIG of each of the components of the regimen. These so-called "cycle sigs" are a property of the regimen, although there are some cases where different components of a regimen have different cycle sigs (e.g., chemoradiotherapy often has different timing parameters for the chemotherapy and the radiotherapy parts). In the OMOP version of the HemOnc vocabulary, these instructions are captured as character strings; we are also in the process of digesting them into component parts.
- Examples: 14-day cycle for up to 8 cycles, 21-day cycle for 4 cycles, 21-day cycle for up to 35 cycles (2 years)
Modality refers to the intended effect of the agents being used in the regimen. Note that this can be distinct from the mechanism of action. The classic example is rituximab, which is a chemotherapeutic in the regimen R-CHOP and an immunosuppressive agent when used as monotherapy for immune thrombocytopenia. Other examples are steroids, which can be hormonotherapy, chemotherapy, or supportive medications depending on the intended use. We follow the SEER/NAACCR guidelines for modality, which means e.g., that a chemoradiotherapy regimen will have two modalities (chemotherapy and radiotherapy). In the future, we will develop a combined modality concept class.
- Examples: anticoagulation, chemotherapy, immunotherapy
A regimen is one or more components given concurrently with an intended disease-modifying effect.
- Examples: 7 plus 3d, 7 plus 3d and Midostaurin, R-CHOP
A regimen stub is something that would ordinarily be a regimen, but is missing details such as what are the individual components. The most common reason for this is that the regimen is described on HemOnc.org as a comparator to another regimen but there are no further details. This situation most commonly arises when an experimental comparator arm is not superior to the control arm, thus not meeting the criteria for inclusion on HemOnc.org.
- Examples: FULV and Trimetrexate, Plitidespin and Dexamethasone
Regimen Class (new in version 2020-01-25)
A regimen class is a collection of regimens based on a common theme. Regimen classes enable the aggregation of different but similar regimens, and are often referred to within FDA labels.
- Examples: platinum doublet, bevacizumab-containing regimen
These are US and non-US brand names for drugs.
- Examples: Abatoarin, Acetisal, Aclacin
Components are the granular constituents of regimens. The majority of components in the HemOnc ontology are drugs or biologics, along with a small number of radiation therapy components. In general we use the plain form name of a drug, not the conjugated salt or ester (e.g., sunitinib, not sunitinib malate; doxorubicin, not doxorubicin hydrochloride).
- Examples: abciximab, abemaciclib, abexinostat
Most drug components in HemOnc are members of one or more component classes. These classes are organized primarily by mechanism of action. There are also several classes which are not mechanistic but may be of interest, e.g., WHO Essential Cancer Medicines.
- Examples: 5 alpha-reductase inhibitor, AKT1 inhibitor, anthracycline
Surgical procedures generally performed with the intent of destruction or removal of cancerous tissue.
- Examples: adrenalectomy, lymphadenectomy, interval debulking surgery
These are dispensing instructions specific to radiation oncology prescriptions. We are in the process of breaking down these character strings into constituent parts.
- Example: 1.1 Gy fractions x 70 fractions, given twice per day, 5 times per week (total dose: 77 Gy)
These are the routes by which medications may be administered or taken.
- Examples: intravenous, oral, subcutaneous
These are the dispensing instructions specific to drug prescriptions. In order to quality as a full SIG (as opposed to Sig Stub, see below), the instruction must contain the following: dose, dose unit, route, date. There are in addition several optional parameters, which will be shortly described in further detail. We are in the process of breaking down these character strings into constituent parts.
- Example: 0.4 mg/m^2/day IV continuous infusion over 96 hours, started on day 1 (total dose per cycle: 1.6 mg/m^2)
These are the dispensing instructions specific to drug prescriptions, that are lacking at least one of the four required categories to be designated a full SIG.
- Example: (dose not specified) IT once per day on days 22 and 43
Endpoint (new in version 2020-01-25)
These are endpoints reported by the study, typically the primary endpoint when the study is "negative" and the least surrogate endpoint with P-value <= 0.10 when the study is "positive" for the primary endpoint. More information is [Response to treatment|available here].
- Examples: CR rate after first induction, DFS36, OS, OS50%
- DFS36 = Disease Free Survival at 36 months (fixed interval endpoint)
- OS50% = median Overall Survival (fixed event endpoint)
Experimental design (new in version 2020-01-25)
These are the designs used by the experimental arm(s) in a study. More information is [Experimental design|available here].
- Examples: de-escalation, escalation, in-class switch, out-of-class switch
This is the name of a prospective study conducted to evaluate one or more regimens on a population of human subjects. When possible, we try to use the abbreviated name provided by the authors and/or by ClinicalTrials.gov; these were somewhat uncommon prior to 2010 except for cooperative group studies. However, there are several examples where the same study name is used in different cancer types (e.g., BEACON) and we rename these to avoid name collisions.
- Examples: ABSOLUTE, ACOSOG Z1031, ECOG E3483
Study Class (new in version 2020-01-25)
Right now, the only study class in HemOnc is the FDA registration study.
- Example: FDA registration study
A formal consortium of individuals or institutions assembled for the purposes of running large multi-site studies.
- Examples: Eastern Cooperative Oncology Group, EINSTEIN Investigators, EORTC Children Leukemia Group
Study name short
By convention, this is the last name of the first author, followed by "et al." followed by the year of the publication. For year, we use the year of e-publication when there is an e-publication ahead of print. If there are two authors, the convention is "Last Name #1" & "Last Name #2" Year. When there is one author, the convention is "Last Name" Year. Note that when there is no abbreviated name, the Study name is the same as Study name short.
- Examples: Adelstein et al. 2003, Adelstein et al. 2010, Alberts et al. 1989
The peer-reviewed journal in which a study is published, using the standard MEDLINE abbreviations.
- Examples: Blood Adv, N Engl J Med, Ann Oncol
Most of the references included in the HemOnc vocabulary are also indexed in MEDLINE. When this is the case, we also include a direct hyperlink to the PubMed abstract.
This is the name for a published report on a study, using the following naming convention: Study::Sequence, where Sequence == 00 is the primary publication, Sequence == 01 is the first update, etc.
- Examples: ABSOLUTE::00, Abrey et al. 2000::01
This it the title of the published report on a study.
- Example: A comparative study of two regimens of combination chemotherapy in acute leukemia
This is the direct hyperlink to the publication described by the Reference concept.
Author names, in the format of Last-Name_First/Middle.
- Examples: Abbruzzese_Alberto, Abbruzzese_James L, Abernethy_Amy
Examples: 1946, 2020