**NCI Thesaurus**

**Apelon TDE**

**Editing Procedures**

**and Style Guide**

**March, 2007**

**Version 3.23**

#### **Apelon TDE Editing Procedures and Style Guide**

### General notes

[Getting Started](#gettingstarted)

[Overview of the Editing
Environment](#overview-of-the-editing-environment-and-editing-cycle)

## [Anatomy of a Concept](#anatomy-of-a-concept-1)

[Concept Name](#concept-name)

[Kind](#kind)

[Code and ID](#code-and-id)

[Super Concept](#super-concept)

[Role](#role)

> [Primitive and Defined](#primitive-and-defined)

###### [Property](#property-1)

> [Complex Property](#complex-property)
>
> [Full Synonym](#full_synonym)
>
> [Reciprocal Property](#reciprocal-property)
>
> [CUI](#cui)

[TDE Search Function](#search)

[Editing Procedures](#editing-procedures)

[Creating Concepts](#creating-concepts)

[Treeing Concepts](#treeing-concepts)

[Adding Atoms](#adding-atoms-to-concepts)

[Changing Atoms](#changing-existing-atoms)

[Deleting Atoms](#deleting-atoms)

[Definitions](#definitions)

# [Changing Definitions](#changing-definitions-1)

[Semantic Type](#semantic-type)

[Splitting Concepts](#splitting-concepts)

[Merging Concepts](#merging-concepts)

[Retiring Concepts](#retiring-concepts)

[Modeling](#modeling)

[Modeling Principles](#modeling-principles)

[Classification](#classification)

## [Workflow Procedures](#workflow-procedures-1)

[Style](#style-etc.)

[Information Sources](#info)

[Inclusion Criteria for Diseases](#inclusion)

[Addition of caDSR Terminology - Use Cases](#caDSRusecase)

[Appendices](#appendix)

##### [Kinds](#kinds-1)

##### [Term Sources](#subsources)

##### [Term Types](#termtypes)

##### [UMLS Semantic Types](#umls-semantic-types-1)

This document is intended as a guide to using the Apelon Terminology
Development Environment (TDE), as implemented by the National Cancer
Institute (NCI), for development and maintenance of the NCI Thesaurus
(NCIt). The basic Apelon application has been adapted and extended to
meet the specific needs of NCI Enterprise Vocabulary Services (EVS).
Therefore, many of the procedures outlined here do not pertain to other
TDE systems.

NCI EVS has a policy of using open-source tools wherever possible.
Future development of NCIt will utilize the Protégé editing environment,
as adapted for NCIt. Most of the features and functions outlined here
will also exist in Protégé but the specific procedures for use may
change.

**[General notes about the system]{.underline}**:

[]{#gettingstarted .anchor}**[Getting Started]{.underline}**:

Each Editor/Modeler will have installed:

> ApelonTDEProfessional3.0
>
> ApelonCustomWFModeler
>
> NCI Code Generator
>
> NCI ID Generator
>
> Edit Filters
>
> Extensions

The TDE Professional editing environment is composed of three separate
programs:

> OntylogEditor: the editing interface.
>
> DataManager: used to export, import, and classify the database. Export
> and import are generally done by the workflow manager and
> classification can be done within OntylogEditor. Therefore, you likely
> will not need to use this program.

SchemaManager: sets up the needed data tables on the server. This is
done by the workflow manager so you shouldn\'t need to use this program.

**Settings for connecting**:

User: your user name -- you will get this from the Workflow Manager

Password: your password -- you will get this from the Workflow Manager

Host: cbiodb10.nci.nih.gov

Click \'Advanced\'; Set \'Instance\' to \'evsdb\'

Advanced/Port: leave set to1521

The Work Manager will issue you a \"Workflow Modeler Ticket\". This will
arrive by email. The attachment \<*username*.TICKET.xml\> should be
saved to the bin folder within your TDE Professional directory on your
hard drive:

> Open your email document and right-click on the attachment
>
> Choose \'Save as\'
>
> Navigate to TDE Professional\\bin
>
> Click \'OK\'

After starting the OntylogEditor for the first time (Start\> Programs\>
Apelon\> TDE Professional\> OntylogEditor) a workticket window will
display (if it doesn\'t: from the \'Tools\' menu choose \'Workflow
Modeler Ticket\'); click \'Import\' and browse to the correct ticket,
select it, then click \'Open\'; then click \'OK\'.

If you are an editor that works on multiple projects, you may have a
different Workflow Modeler ticket for each.

Once you\'ve imported a workflow ticket it shouldn\'t matter what
computer you work from.

### Overview of the Editing Environment and Editing Cycle

Each editor has his own instance of the database and essentially works
in isolation from the other editors; the editing that you do is not seen
directly by other editors. Periodically you will submit *change sets*.
The Workflow Manager receives these change sets for inclusion in a new
*baseline*. After this baseline is distributed all changes become
visible to all editors. In reality, things are more complicated. If two
editors make changes to the same concept and leave it in different end
states, then the workflow software flags the concept as being in
*conflict* and it must be reviewed for *conflict resolution*. The
manager may accept one editor\'s version in total, thereby rejecting the
other\'s changes. The manager may accept some changes from each editor
or reject all changes or make other or additional changes. Thus, in the
next baseline the concept may not reflect (all) the changes you made.
The Workflow Manager must also review and OK concept retirements ([see
below](#retiring-concepts)).

Vocabulary users do not directly see the database we edit. Rather, once
a month, our developmental database is \"published\" for end-user use.
The published version will be derived from the baseline created on the
final Friday of each month. An interim developmental baseline update
will usually be made in the middle of the month. A day or so before an
update you will receive an email telling you when the baseline update is
to be done and a deadline for submitting change sets. After this
deadline do not resume editing until you have received an email or
verbal communication saying that it is OK to do so.

### Anatomy of a Concept

A concept is the basic unit of information contained in the Thesaurus.
They describe sets of individuals in a given domain. A concept has a
name, belongs to a Namespace and exists in relation to other concepts.
Each concept is composed of various types of information as described
below:

### Concept Name

Concept Name is one of three ways the software keeps track of concepts,
each of which must be unique within the database (the others are Code
and ID, [see below](#code-and-id)). It is also the way that concepts are
represented to editors in the editing interface. In contrast, concepts
are presented to users by our Preferred Name, but they can see the
concept names in download files and as additional information on
browsers. It is not necessary that the concept name be completely
meaningful. Instead, it is required that it be unique within our
database and it needs to be explicit enough so that the editors will
have a good idea what the concept is (i.e., it should have *face
validity*). It is critical that Concept Name be unchanging but Preferred
Name may be changed as necessary. For reasons of OWL (Ontology Web
Language) compatibility it is necessary that all punctuation besides
underscore and dash be avoided. Our standard form for concept name is
\"Title_Case_with_Underscore_Separators\".

Concept name and preferred name will generally be singular. See
[Style](#style-etc.) for additional guidelines.

Once created a concept name **MAY NOT** be changed. Therefore, when
creating a concept make sure that it is what you want and that it is
spelled correctly.

Edit filters ensure OWL compliance and prevent concept renaming.

Concept name is displayed in **black** as the first line in an edit
panel.

\*\*\*Please note: after we begin using Protégé/OWL and the LexBIG
server only Concept Code will need to be unique. Only Concept Code is to
be used as annotations in external systems.

### Kind

Kinds are types. By definition, kinds are all pairwise disjoint from one
another. In other words the sets of individuals of a given kind have no
overlap with any other kind (i.e., *Orthogonal* (mutually independent,
well separated, non-overlapping). Kinds are maintained in separate
trees. A concept must have a kind, but can only have one kind.

Kind will only be *stated* for the concept at the top of the tree. All
concepts below will inherit this kind, and will show their inherited
kind. If you move a concept from one tree/kind to another, the kind
automatically changes when the new *Super Concept* has been added The
software will not allow you to retree a concept with children if it will
cause a kind change. Contact your Workflow Manager if this seems
necessary.

A Reference Kind is a tree or vocabulary that originates from another
source and is not maintained or edited by us; it is accepted as is. It
is there for us to use for *Role Values*.

Kinds are displayed in **teal**.

### Code and ID

These are generated by the editing software during concept creation.
They cannot be changed through the editing interface. NCI end users are
advised to use \'Code\' as their reference in all applications.

Code and ID are displayed in **grey**.

### Super Concept

Concepts are organized into hierarchical trees. With the exception of
the top concepts each concept is a subtype of another concept. Concepts
are often said to have parent-child relationships. In the vernacular of
the TDE the parent is called a \'Super Concept\'. The top level terms
are sometimes called roots and the terminal concepts leaves. Any concept
inbetween may be called a node.

Super Concept is displayed in **blue**.

### Role

A Role is a non-hierarchical, named relationship between concepts. They
are binary relationships pointing from one concept to another concept.
Roles are unidirectional and each role has a *Domain* and a *Range*; the
role points from one kind, the domain, to another (or same) kind, the
range. The specific concept pointed to is considered the *Role Value*.
Each kind will have a specific group of roles, restricted by domain
(Kind). Attempting to apply a role from another domain will generate an
error message when you try to save your work.

A concept will inherit the *assertions* made by roles for its parent. In
general a role should be stated as high on a tree as possible and
allowed to inherit. Inherited roles are not seen in the Edit Panel,
which shows a concept\'s *stated view*, but can been seen in the
\'Inferred Concept\' panel.

Roles are displayed in **green**.

#### Primitive and Defined

The sum total of a concept\'s tree position plus its roles (stated or
inherited) equals the concept\'s definition. Every concept is either
*Primitive* or *Defined*. The difference between a primitive concept and
a defined concept is the completeness of the definition; primitive
definitions are not complete. For each kind we specify a minimal set of
roles that must be filled for a concept to be considered Defined. We
assert that this group of roles is necessary and sufficient to provide a
complete definition of the concept: the computer-generated definition.
These are considered *Defining Roles*. All other roles are considered
non-defining roles. The idea of defining and non-defining roles is a set
of rules we impose. The software does not recognize any distinction; all
roles contribute to the computer definition. When all defining roles
have been filled the concept can be considered *Defined* and should be
designated as such by toggling from *Primitive* to *Defined* and saving
the changes. Changing the state of a concept from primitive to defined
allows the software to generate computer-guided tree positions for a
concept based on its definition (see [Classification](#classification)
below). Some concepts serve as headers in the hierarchies. These will
usually be too general to be defined.

Please note that the computer generated definition should not be
confused with the english-language definitions we create. Our text
definitions are not machine interpretable and are not used by the
software.

The state of a concept is displayed in **yellow**.

#### Role Modifiers

\--Section coming soon

### Property

A property is information about a specific concept. Properties do not
inherit. In the software they are stored as strings (so, even if they
match a concept name they do not point to the concept in the way that a
Role does).

Properties are displayed in **purple**.

#### Complex Property

Our uses require that some properties contain both a value and
additional information about the value. The most common types of this
information are \"Source\" and \"Term Type\". This information is
carried in Property Qualifiers.

At present we have two complex properties:

#### FULL_SYNONYM

Each full synonym (FULL_SYN) consists of a term and additional property
qualifiers for term type (Syn_Term_Type), term source (Syn_Term_Source),
and may also have a term code (Syn_Source_Code). Term code is optional
and only applies to some sources. This structure is enforced by an edit
filter. We often refer to full synonyms by the UMLS term \"atom\".

#### 

#### Term Type

> The term type indicates a particular \"meaning\" of a term. The most
> common are \'Preferred Term\' (PT) and \'Synonym\' (SY). By default a
> term is assumed to be a synonym unless otherwise specified; no
> Syn_Term_Type need be specified for a synonym. For any term source
> present there should be a single PT atom but a concept may have
> several (different) PT\'s from different sources. See appendix for the
> full list of [term types](#termtypes) and their meanings.

#### 

#### Term Source

> A term source is a group or division within NCI, or an outside
> contributor, that has supplied terms to the EVS and who needs to
> preserve these terms for their purposes. Some sources will require a
> term code; NCI does not. Terms from any source other than NCI should
> not be changed without permission; neither should they remain in a
> retired concept. By default a term is assumed to be NCI source unless
> otherwise specified; no term source should be specified for an NCI
> term. See appendix for a full list of [sources](#subsources).

[DEFINITION]{.underline}

The definition property hold the official NCI definition for a concept.
Each definition consists of a text definition and additional property
qualifiers for Definition_Review_Date and Definition_Reviewer Name.
Optionally, a Definition_Attribution may also be specified. The
definition text is limited to 1024 characters and spaces. All effort
should be made to stay within this limit. However, if this should prove
impossible the definition should be specified as a LONG_DEFINITION, with
the same qualifiers as a definition. Definitions from a source other
than NCI will be specified as ALT_DEFINITION or ALT_LONG_DEFINITION. In
addition to the qualifiers already mentioned these will also need
Definition_Source. See appendix for a list of [allowable definition
sources](#defsource-1).

#### 

#### 

#### Reciprocal Property

Attempting to model concepts such that they have roles that point back
and forth between them (e.g., \'Gene Encodes Protein\' \<-\> \'Protein
Encoded By Gene\') is not allowed by the software and results in a
*Cycle Error* during *Classification*. Since this may be useful and
important information it will be represented by a *Reciprocal Property*.
So, for example, the role \'Gene Product Encoded by Gene\' would have
the \"Reciprocal Property\" \'Gene Encodes Product\'. These must be
created by the editor. Make sure that the string exactly matches the
preferred name of the protein. If the protein gets renamed you must edit
the Encodes_Product property to match.

#### CUI

CUI is an abbreviation for \"Concept Unique Identifier\". In the Unified
Medical Language System (UMLS) it is meant to be an unchanging label for
a concept. It is maintained in the property \'UMLS_CUI\' or
\'NCI_META_CUI\' as a means to map NCI concepts to UMLS concepts. CUI\'s
are not to be changed without permission.

### The TDE Search Function

By default, the search function only searches the Concept Name field. It
is important to keep in mind that the search function is completely
literal. It does not search for lexical variants (word order
differences) or singular and plural (normal-form search). Punctuation,
spelling, and spacing must match exactly (e.g., a search for
\"gallbladder\" will not find \"gall bladder\"). However, \* (asterisk)
works as a wildcard, so a search for \'gall\*\' would return either. It
would also find \"Gallbladder Carcinoma\", \"Gallbladder Polyp\",
\"Gallium Nitrate\", etc. Full synonym and preferred name are not
searched unless specifically selected; click the \'Property\' tab, check
the Property box and then select FULL_SYN and \'Preferred_Name\' by
ctrl-click (additional properties can be simultaneously searched by
selecting multiple properties by control-click or shift-click). By
default a maximum of 10 results will be returned. This can be changed to
50, 100, 250, or ALL.

A \"Normal Form Search\" is available. This function will ignore word
order and perform some word completion. To use this, \'Normal Form
Search\' must be selected in the search options. When checked you will
be presented with a list of the Properties for which normal form
searching is enabled. Use shift-click or ctrl-click to select multiple
properties.

All search parameters need to be set separately in the Search panel and
the Search dialog window, and need to be reset each time you launch the
program.

## [Searching for existing concepts, especially before creating new concepts]{.underline}

It is essential that you do a thorough search for existing concepts
before you create a new concept. This is to avoid a \"duplicate now,
merge later\" scenario.

> Always search for Concept Name, Preferred_Name, Display_Name and
> FULL_SYN
>
> in the search panel use \'Search as text\' and check \'Name\'. Also
> select the Property tab, check \'Property\' and then select
> Preferred_Name and FULL_SYN by ctrl-click. This needs to be reset
> every time you launch the editor.
>
> Get into the habit of searching for:
>
> \- the exact term string
>
> \- variants and synonyms
>
> \- identifiers such as gene symbol, CAS number, etc
>
> \- \"subterms\"; core parts of a longer string:
>
> example 1: in a search for \'Activated p21cdc42Hs Kinase\' also search
> for \'\*Activated\*\', \'\*Activated\*Kinase\*\", and \'\*Kinase\*\'
>
> example 2: in a search for \'Beta-Adrenergic Receptor Kinase 1\' also
> search for \'\*Adrenergic Receptor\*\", \'\*Receptor Kinase\*\', and
> \'\*Receptor\*Kinase\*\'

Unfortunately, such searches could return many hits to look through.
It\'s necessary and unavoidable.

###  

### Editing Procedures

While editing always keep in mind:

> Consistent meaning of all atoms. If necessary, split the concept to
> establish true synonymy (see [Splitting Concepts](#splitting-concepts)
> below) or move atoms between existing concepts
>
> Correct spelling in all properties
>
> Correct spelling and grammar of definitions -- all definitions should
> start with a Capital letter and end with a period.
>
> Correct semantic type
>
> Correct preferred term
>
> Correct capitalization of atoms: Title Style: first letter of each
> word in Caps except for with/and/of, etc.

Once a concept has been created nothing should be done to it that
substantially changes its meaning. Changing the preferred name should
only be done if it does not change the meaning of the concept. Retreeing
a concept should only be done if it does not change the meaning of the
concept. Retreeing a concept to another tree or another kind will almost
certainly change its meaning. Create a new concept if necessary.

All additions to the database **must** be spell checked.

### Creating Concepts

A new concept should be created when it is determined that no existing
concept is adequate or appropriate. Never create a new concept until you
have made a thorough search to determine if the concept, or an
equivalent variant, already exists. Think of different ways that the
concept may be expressed and search for each (e.g., search both for
\"protein\" and \"gene product\"). Always search concept name, preferred
name, and full_syn. [See above](#search).

When creating a new concept try to choose concept name so that it has
face validity and it is readily apparent how the concept differs from
any similar concepts in the database (e.g., Cyclin Kinase Inhibitor
(naturally-occurring factors) vs. Cyclin-Dependent Kinase Inhibitor
**Drug**). Please remember that concept name and preferred name will
generally be singular and that the concept name must be OWL compliant
([see above](#concept-name)). See [Style](#style-etc.) for additional
guidelines. It is allowable that multiple concepts have the same
preferred name (e.g., \'Fish\' the animal and \'FISH\' the technique)
but their concept names must be unique.

> **Procedure:**

1)  In a Word document type the term and do spell checking. Copy the
    term;

2)  In TDE click the \"New\" button and paste the preferred term into
    the dialog box. This creates the concept name. Be sure to follow the
    concept name rules ([see above](#concept-name)) ; once created the
    concept name shall not be changed. The property \'Preferred_Term\'
    must be filled separately and will not necessarily match the concept
    name; a corresponding FULL_SYN, qualified with Syn_Term_Type of PT,
    must be created.

3)  Tree the concept: you must assign a Super Concept ([see
    below](#treeing-concepts)).

4)  Assign a Semantic Type ([see below](#semantic-type));

5)  Add additional atoms (e.g., synonyms) as needed: type the term in
    Word, spell check, and copy; paste into the dialog box; repeat as
    necessary. Be sure to follow the format for complex properties;

6)  Model the concept as necessary ([see below](#modeling));

7)  Provide an english language definition ([see below](#definitions));

8)  When finished, click \'Save\'.

### Treeing Concepts

Every concept must have a parent concept (Super Concept). You should
always try to tree a concept in the most specific place. For example, a
Helicase is a kind of enzyme but more specifically, it is a type of
hydrolase. Therefore, it should be treed only as isa Hydrolase. Once
treed a concept inherits all of the attributes of its parents.
Therefore, by inheritance a Helicase is also a hydrolase, an enzyme, and
a protein. If a concept is treed in the correct position then you should
be able to walk all the way back up the tree to the top and have each
assertion be true. If any one assertion is not true (or sometimes not
true) then the concept is in the wrong place.

As a general rule, multiple treeing of a concept is OK but should be
kept to a minimum. Whenever possible a single parent should be chosen
and all other assertions should be made through a Role. Remember that a
concept can only have one kind. Therefore, a concept can only be double
treed within a single kind/tree. If a term has two distinct meanings,
requiring treeing in multiple kinds, there must be two concepts rather
that one concept treed in two places.

### Adding atoms to concepts

Atoms are added to existing concepts to add new synonyms or additional
term groups or term sources.

> **Procedure:**

1)  Type the term in Word and do spell checking. Copy the term;

2)  Use \'Add New Property\' to select FULL_SYN; paste the term into the
    dialog box; repeat as necessary. Be sure to follow the format for
    FULL_SYN ([see above](#full_synonym));

3)  When finished, click \'Save\'.

### Changing existing atoms

Changes are made to an existing atom when it needs to be altered (e.g.,
addition of a qualifier such as \"Gene\" or \"Protein\", to correct a
spelling error, capitalization problem, or singular/plural form, or to
change the term group or term source). Only NCI-source atoms are to be
touched. All others are to be maintained as is.

> **Procedure:**
>
> To change the string:

1)  Right click the atom (or qualifier) to be changed and choose
    \'Change value\';

2)  Make the necessary change in Word and do spell checking;

3)  Copy the altered atom and paste it into the property dialog box;
    click \'OK\'; repeat as necessary;

4)  When finished, click \'Save\'.

### Deleting atoms

Atoms should be deleted to remove duplicates, errors, etc. Only
NCI-source atoms are to be touched. All others are to be maintained as
is.

> **Procedure:**

1)  Right click the atom to be changed and choose \'Delete\'; repeat as
    necessary;

2)  When finished, click \'Save\'.

### Definitions

General considerations:

The goal is for each concept to have one good technical NCI definition
(DEFINTION). Many concepts will also require one NCI-GLOSS lay
definition (ALT_DEFINITION, NCI-GLOSS source). Some other special
definitions may also be necessary (e.g., ALT_DEFINITION, FDA source).
Only NCI-source definitions may be altered. However, NCI-GLOSS
definitions can be deleted if they are inaccurate or duplicated.

A definition should be composed in a word processing program, spell
checked, and then copied and pasted into the TDE. It should start with a
capital letter and end with a period. Double spaces are only allowed
after a period.

> **Attribution of sources/Copyright issues**
>
> For most sources copyright issues with \"borrowed\" definitions have
> not been worked out.
>
> Sources are attributed using the Definition_Attribution qualifier.
>
> If a definition is taken directly from a source, without change, the
> source must be cited (e.g., American Heritage Dictionary, On-line
> Medical Dictionary). If minor changes are made to a definition it
> should be cited as \"from \<source\>\". If a definition uses a source
> as a recognizable base and then elaborates further it should be cited
> as \"from \<source\> and NCI\". If a definition is highly reworked
> such that it is no longer recognizable as from the original source it
> can be considered as NCI. If a definition is cobbled together from
> several sources and resembles none it can be considered as NCI. If you
> write a definition off the top of your head it is considered NCI. The
> NCI is not attributed by a qualifier. If you encounter a definition
> with an attribute specified within parentheses in the definition text
> it should be moved (without parentheses) to a Definition_Attribution
> qualifier. Again, NCI is not attributed.

When using a journal article as a source, cite the article (e.g., \"Jaju
et al. Genes Chromosomes Cancer 1998. 22:251-256\").

> When using a website as a source provide enough information so that
> someone can, hopefully, find their way back and evaluate the source
> (e.g., \"Lymphoma Information Network glossary\",
> \"<http://www.lef.org/prod_hp/abstracts/biostimabs.html>\",
> \"MedicineNet\", \"Chemical and Physical Carcinogenesis Branch, DCB
> homepage\")
>
> Stedman definitions are for internal use only and should not be used.
> If you see an NCI definition citing STED rework it or replace it as
> necessary.
>
> Dorland and Devita are copyright protected and should not be used.
> Rework or replace if found.

Sometimes it will be necessary to record descriptive information about a
concept that is not really a definition. This could be instructions to a
coder about how and when a concept is to be applied or it could be notes
from one editor to another about why a concept is treed where it is,
additional information needed, etc. This information should not be put
in a definition. Instead, use \'DesignNote\' or \'Editor_Note\',
respectively. Editor_Note is purely for use by editors and is not
revealed to users.

Definitions have a limit of 1024 characters and spaces.

### Changing definitions

Only NCI-source definitions (DEFINITION) may be altered.

> **Procedure**: Make all changes in Word. After spell checking, copy
> the changed definition and past it into the property \'Change value\'
> dialog box. Be sure to follow the format for Definition.

### Semantic Type

The Semantic Type is the basic category or categories that describe a
Concept. In general, applying semantic types aids in allowing users (or
computer programs) to draw conclusions about concepts by virtue of the
categories to which they have been assigned. We use a set of Semantic
types developed for the UMLS Metathesaurus. There are currently 134
Semantic types in the UMLS (see in [Appendix](#appendix)). The Semantic
types are organized in a hierarchy. The top of the hierarchy has two
nodes, \"Entity\" and \"Event.\" Each semantic type appears in only one
location within the hierarchy.

General Rules On applying Semantic Types (from UMLS):

-   Apply a particular Semantic type only if the concept has an \"is_a\"
    relationship to that type. For Example:

```{=html}
<!-- -->
```
-   Agaricales is_a \"Fungus\"

-   Mushroom Poisoning is_a \"Injury or Poisoning.\" Mushroom Poisoning
    is NOT a \"Food.\"

-   Mushroom Poison is_a \"Hazardous or Poisonous Substance.\" Mushroom
    Poison is NOT an \"Injury or Poisoning.\"

-   Shiitake Mushroom is_a \"Fungus\" and is_a \"Food\"

```{=html}
<!-- -->
```
-   It is important to read the definition and usage notes for each
    Semantic type. It is not possible to rely solely on the name of the
    Semantic type, since there are often shades of meaning involved. The
    definition (attempts to) makes clear the intended meaning in the
    UMLS context.

```{=html}
<!-- -->
```
-   In general a concept should be assigned only one Semantic type. An
    exception is Chemicals where separate semantic types for structure
    and function will usually be applied. Example: Aspirin: is_a
    \"Organic Chemical\" and is_a \"Pharmacologic Substance\"

```{=html}
<!-- -->
```
-   Assign types according to the primary meaning of the concept.

```{=html}
<!-- -->
```
-   Do not assign both parent and child Semantic types from the
    hierarchy.

> If all children apply, then assign the parent.
>
> If only some children apply, then assign the more specific type as
> appropriate.

All concepts must have at least one Semantic type.

> **Procedure:**
>
> Choose \'Add New Property\': \'Semantic_Type\'. Use the picklist to
> choose the most appropriate semantic type; they are listed in the same
> order as the UMLS hierarchy. Click \'OK\'. Click \'Save\'.

### Splitting Concepts

A concept should be split when it is determined that not all atoms have
the same meaning, that multiple concepts are represented. This may be
because of error or due to new understanding. A new concept will be
created and the appropriate atoms and attributes will be moved to the
new concept. The new concept will automatically become a sibling of the
original concept and will automatically inherit all of the children of
the original concept. The validity of these inherited relationships must
be reviewed.

Splits are done by enacting the split extension. While this window is
open all other windows and functions of TDE are disabled. Everything
must be done through the Split Concepts interface.

> **Procedure**:

1)  click on the \'Tools\' menu and select \'Split\';

2)  in the new \'Split Concept\' window click \'Search\';

3)  in the new \'Search Concept\' window type the search string and
    click \'Search\'; please note that only the concept name is
    searched;

4)  select the correct hit and drag it to the \'Original Concept\' panel
    of the \'Split Concept\' window (it may be necessary to drag the
    search window aside to have access to the Split window). Close the
    \'Search Concept\' window;

5)  on the \'New Concept\' side of the window click \'New\'; type the
    Concept Name for the new concept and click OK;

6)  drag the appropriate atoms and attributes from the Original Concept
    panel to the New Concept panel. As necessary, delete atoms and
    attributes from the Original Concept. When done click \'Save
    Concepts\'. You are returned to the standard TDE interface;

7)  At this point it may be necessary to do additional editing to the
    original and new concepts. In particular, you should check the
    children and retree them as necessary.

Note: if atoms present in a concept rightly belong in another existing
concept they may simply be moved between concepts. No splitting is
required.

### Merging Concepts

Concepts should be merged when it is determined that they are synonymous
(i.e., they don\'t have a meaning distinct from each other or they are
identical to an already existing concept). Unless otherwise specified,
by default, the older concept (lower code) will survive and gain all of
the roles, properties, parents, and children of the newer concept and
the newer concept will be retired. It is OK to override this if:

1)  The newer concept has been referenced in more cde\'s;

2)  The newer concept is better formed or more fully modeled.

Please note that a merge should \*NOT\* be used to change the concept
name of an otherwise adequate concept. Instead, this can be functionally
achieved by changing the concept\'s preferred name.

Merging is a two step process. First, the editor will \"flag\" a concept
for merging. During this process the concept will gain a parent of
\'Merged *kind* Concept\' within its tree and a Merge_Target property.
Next, during baseline update the Workflow Manager will review all of the
candidate merges. The manager may accept or reject the suggestion. If
accepted the concept properties and role will be transferred to the
merge target concept and the concept will get moved to a \'Retired
Concept\' tree and have its kind changed to \'Retired_Kind\'.

Merges are done by enacting the \'Flag Concepts for Merge\' extension.
While this window is open all other windows and functions of TDE are
disabled. Everything must be done through the \'Flag Concepts for
Merge\' interface.

> **Procedure**:

1)  click on the \'Tools\' menu and select \'Flag Concepts for Merge\';

2)  the \'PreMerge Concepts\' window presents two panels. In either
    panel click \'Search\';

3)  in the \'Search Concept\' window type the concept name for one of
    the concepts to be merged and click \'Search\'; please note that
    only the concept name is searched;

4)  select the correct hit and click \'Select\';

5)  in the other panel click \'Search\'; repeat search and selection for
    second concept to be merged. The older concept will automatically be
    moved to left panel if necessary; click \'Switch\' if there is
    compelling reason to override the default;

6)  Click \'PreMerge\'; a window for editor and design note will pop up;
    you can probably leave these as the default values; click \'OK\'

7)  At this point none of the properties or roles will have been
    transferred to the winning concept. SO that the final result will be
    as you intend it is likely that additional editing to the winning
    and losing concepts will be needed. In particular, you should check
    the parents and children and retree as necessary, and check for
    redundant or inaccurate FULL_SYNs, Semantic_Types, definitions, etc.
    Any non-NCI atoms should be deleted from the retired concept.

### Retiring Concepts

Once a concept has been created and published it is available to users
for coding purposes. Therefore, a concept must never \"disappear\".
Rather than being deleted they are \"retired\". Concepts should be
retired when it is determined that they are unneeded (e.g., another
existing concept has the same meaning or the concept is meaningless or
is an unneeded header). Retirement is a two step process. First, the
editor will \"flag\" a concept for retirement. During this process the
concept will be retreed as a \'Retired *kind* Concept\' within its tree
(Pre-retirement). Next, during baseline update the Workflow Manager will
review all of the preretirements. The manager may accept or reject the
suggestion. If accepted the concept will get moved to a \'Retired
Concept\' tree and have its kind changed to \'Retired_Kind\'. [Once
retired a concept shall not be unretired. Nor shall it be further
edited]{.underline}. If you find a concept.that you feel has been
retired in error, please contact the Workflow Manager.

Pre-retirement is done by enacting the Preretirement extension. While
this window is open all other windows and functions of TDE are disabled.
Everything must be done through the Preretirement interface.

> **Procedure:**

1)  click on the \'Tools\' menu and select \'Flag Concept for
    Retirement\';

2)  in the \'Preretirement\' window click \'Search\';

3)  in the \'Search Concept\' window type the search string and click
    \'Search\'; please note that only the concept name is searched;

4)  select the correct hit and drag it to the left panel of the
    \'Preretirement\' window (it may be necessary to drag the search
    window aside to have access to the Preretirement window).

5)  If the concept to be retired has been used as a role value or if it
    has children these will be indicated in color. It is necessary to
    resolve these before Preretirement. Drag the indicated problems to
    the right panel and remove or redirect the linking role, or retree
    as necessary. After saving, the resolved problem will show in
    italics in the left panel.

6)  Click \'Accept\' to flag for retirement; fill in the requested
    editor note and design note and then click \'OK\'. If you
    **immediately** realize that this retirement was done in error you
    can click \'Unretire\' to restore the concept. You lose the ability
    to unretire as soon as you close the Preretirement window.

If a concept is created and flagged for retirement but the concept has
never been published then it can be deleted before publication of the
next baseline. The editor should alert the Workflow Manager when this
situation applies and the manager will do the deletion. Only the
Workflow Manager can delete a concept.

### 

### Modeling

Modeling establishes assertions about a concept. One assertion is its
tree placement. Additional assertions are created through the use of
Roles.

The primary goal of modeling is to fully distinguish and *Define* every
concept (see [Primitive and Defined](#primitive-and-defined)). When all
defining roles have been filled the concept is considered defined and
should be designated as such. During classification ([see
below](#classification)) each defined concept will be compared to
determine if it has a unique, computer generated definition based on its
tree position and roles (both stated and inherited). Concepts failing
this test will be flagged as \'Equivalent\' and an \'Equivalence Error\'
will be generated. In practice, concepts near the tops of the trees will
remain primitive as will some leaf nodes.

As a secondary goal, filling the optional (non-defining) roles will
represent known information about a concept that may be useful in
linking data or storage and retrieval of documents, thereby aiding in
research.

The actual process of modeling is rather like \"fill in the blanks\".
Each area of interest will have a group of roles and properties
available for use. Some will be designated as \"Defining\" and every
effort should be made to fill these. Others will be considered
non-defining and optional. These are to be filled when the information
is relevant and easily obtained. Run down the list of roles and
properties and fill what you can. If it is taking more than 30 minutes
(on average) to model a concept you are probably digging too deep. Some
information just isn\'t known yet.

Sometimes, you will find that the right concept does not exist for use
as a role value. When this happens you should create the needed concept
(see [concept creation](#creating-concepts) above). An exception is when
the needed concept falls outside of your area of responsibility and
expertise (e.g., if you are an NCI molecular biologist don\'t create new
neoplastic diseases concepts). In this case, note the needed
concept/info in an \'Editor\'s Note\' and talk to the proper person
about creating a concept.

Six ways to add Roles:

1)  with wells showing drag: role value into a role well;

2)  with wells hidden: drag role value into edit window, press ctrl and
    release mouse button, select \'Add New Role\';

3)  right click on concept name and use \"Add New Role\";

4)  drag a role from one tree editor panel to another;

5)  drag recent change into the tree editor panel;

6)  using Form Editor.

Six ways to add Properties:

1)  with wells showing: drag concept into a property well;

2)  with wells hidden: drag concept into edit window, press ctrl and
    release mouse button, select \'Add New Property\';

3)  right click on concept name and use Add Property;

4)  drag a property from one tree editor panel to another;

5)  drag recent change into the tree editor panel;

6)  using Form Editor.

### Modeling Principles

##  If forced to choose between rigor and familiarity or comfort, choose rigor.

> Roles should be asserted at as high a tree level as possible and be
> allowed to inherit to subordinate concepts. To do this properly you
> must consider whether the assertion will be true for **ALL** children.
> If the tree placements are correct but the assertion is only true for
> some children, then the assertion must be made at a lower level. Such
> an assertion is likely to be a discriminating factor in establishing
> subclasses.
>
> When creating roles, the level of abstraction of concepts at each end
> should be comparable (e.g., pointing from a header to another header,
> or a leaf to a leaf, but usually not from a header to a leaf or visa
> versa).
>
> Processes must have either an explicit change in state or involve the
> passage of time. Single states are likely to be findings.

##  Try to enforce \"linguistic consistency\" in names (e.g., \'Blood Cell\', \'Stem Cell\', and \'Schwann Cell\', not \'Cell of Epithelium\')

##  Semantic type homogeneity as a hierarchy desideratum.

> Distance one links easier to make (e.g., \'Protein Encoded By Gene\'
> is easier to verify and establish than \'Protein Malfunction
> Associated with Disease\').
>
> Represent only \"clinically accepted\" gene or protein to disease
> links.

##  To the extent possible, processes should be split from any anatomic structure.

### Classification

Classification is the machine process whereby every concept has a
computer generated definition created for it. Several things happen
during classification. First, inherited (inferred) roles are computed.
Second, the definitions for defined concepts are compared for uniqueness
and logical consistency. Third, using the logical rules of inference
that govern our description logic the logical placement of defined
concepts in the hierarchy is determined. The classification process can
reveal direct modeling errors, unintended statements, and discover new
things about existing concepts.

The software can indicate three types of direct errors: Kind,
Equivalence, and Cycle.

> Kind errors can occur if a concept is assigned parents from trees of
> different kinds or when the domain and range of roles are of the wrong
> type for a concept kind. In practice these errors should be caught by
> the software when you try to make these assignment and disallowed.
>
> Equivalence errors occur when the computer generated definitions for
> defined concepts are found to be identical. Since inherited
> information is used in these comparisons these equivalencies may not
> be obvious.
>
> Cycle errors occur when modeling has created a closed loop of roles.
> This could be two concepts with roles pointing directly at one
> another, or loops involving three or more concepts. We try to choose
> the directionality of the roles to minimize the potential for cycles
> but not all possibilities can be anticipated or avoided in the
> planning stages.
>
> ● Classification errors must be fixed. Never generate a changeset
> until after you\'ve classified and determined that all is well.
>
> ● To Classify: Tools\>Classify or click the Classification icon;
> errors will be indicated in the Error Viewer window.

The computer directed reorganization of defined concepts can reveal new
insight about existing concepts and point out logical errors in the
modeling process. It is common that this process will reorganize sibling
concepts into a deeper hierarchy. Sometimes this will point out
something you missed but is true. Sometimes this will be an undesired,
wrong result requiring a change to the modeling or tree structure.

### Workflow Procedures

Editing may be done through Work Assignments or unassigned changes
(\"free range\" or ad hoc editing).

[Unassigned Editing]{.underline}

Most of our editing is done without assignments. Verbal communication or
email instructions will be used to delineate areas of responsibility and
tasks. Your changes will be returned as change sets. Change sets should
be generated and sent at regular intervals (daily is not too often).
**Never return a change set if you have unresolved classification
errors.**

1)  From the \'Tools\' menu select \'Export Change set\';

2)  Click \'Select All\' and then click \'Export\';

3)  When you are asked if you want to mail the change set now, click
    \'No\'; instead, through your Windows Explorer go to your TDE
    Professional\\bin folder. Locate the newest file with the .cs
    extension and \"zip\" it: right click and select the second \'Add to
    zip\' choice (includes the file name);

4)  Send the zipped file to the Workflow Manager as an email attachment.

If you make changes to a concept, save the changes, and then later
decide that these should not have been done there are several ways to
correct the situation:

1.  Edit the concept back to its original state;

2.  Exclude the concept from the export changes **\*and then\*** notify
    the workflow manager of the unexported change(s);

3.  Export the concept(s) in its own changeset, trash it or never send
    it, and then export and send everything else.

#### 

#### Work Assignments

You may receive Work Assignments by email from the Work Manager; the
assignment will come as an attachment. To be accessible for editing the
attachments must be saved to the \'assignments\' folder in your TDE
Professional directory (create this folder if it doesn\'t already
exist). Right click on the attachment, select \'Save As\', follow path:
Program Files\\Apelon\\TDE Professional\\assignments, then click
\'Save\'.

4.  In the Ontylog Editor configure panels to include \"Assignments\":
    Options\> Configure Panels;

5.  The assignments will appear in the Assignments panel. If you
    get/move assignments while your editor is already running with an
    assignments panel you will need to right-click in the Assignments
    panel and \'Refresh\' before they will be visible.

Click the \"plus-box\" of an assignment to reveal a list of concepts
needing editing, modeling, or review. These can be dragged into a Tree
Editor panel or Form Editor panel. After doing whatever is necessary,
and saving, or determining that nothing needs to be done, the concept
can be marked as \"Complete\"

1)  In the Assignments panel, select the concept and right click on it

2)  Select \"Complete\"

When all concepts have been edited and have been marked as complete the
assignment status will show as \'Complete\' and can be returned to the
Work Manager. After completing a modeling assignment, and before
returning it, you will need to classify your database and resolve any
conflicts. **Never return an assignment if you have unresolved
classification errors.**

1.  Highlight the assignment title in the Assignments panel;

2.  Right click on the assignment;

3.  Select \'Export change set\';

4.  When you are asked if you want to mail the change set now, click
    \'No\'. The assignment status will now be \'Exported\' and
    \'Complete\';

5.  Through your Windows Explorer go to your assignments folder. Locate
    the file with the .cs extension and \"zip\" it (see above);

6.  Send the zipped file to the Workflow Manager as an email attachment;

7.  Right-click on the assignment and select \'Mark as Returned\'

Please return assignments as you complete them.

Changes you make to concepts that are not on your assignment lists must
be returned separately through an \"Unassigned Change set\". Even if you
don\'t think you made any unassigned changes you should try to export a
change set. If there are no changes to be exported the window will be
empty. If there are changes, then follow the instructions above for
Unassigned Editing.

Occasionally when you open an assignment all concepts will show as
\"Deleted\". Under normal circumstances when you first open an
assignment the program creates a matching change set file
\<*worklist.username.#.*ASG.cs\> and a matching status file
\<*worklist.username.#.*ASG.stat\>. This \"Deleted\" status happens if
the status file fails to be created, or is otherwise \"lost\". Any edits
you may have already made are still present in your database. To \"fix\"
the assignment, do the following:

1)  Through your Windows Explorer go to your TDE
    Professional\\assignments folder. Delete the files for the damaged
    assignment (ASG, ASG.stat, and ASG.cs) Go back to your email and
    create a new copy of the assignment and paste it into your
    assignments folder;

2)  Return to OntylogEditor and refresh your Assignments panel. The
    assignment should now be OK;

3)  For any concepts that have already been edited double check the
    editing and then mark the concept as \'Complete\';

4)  Continue editing as normal.

### Style, etc.

Both the concept name and preferred name will be singular, except in
special circumstances.

The Concept name should be in \"Title_Case_with_Underscore_Separators\".
The only allowed punctuation marks are dash (-) and underscore (\_). If
the concept name would ordinarily start with a number it must be
preceded by an underscore (e.g., \_1-Nitropyrene)

Avoid using an underscore where an apostrophe would be; instead,
eliminate the space altogether (e.g., Burkitts_Lymphoma instead of
Burkitt_s_Lymphoma)

Preferred name should be \"Title Case with Space Separators\". It need
not match the concept name (e.g., concept Distribution_Activity has
preferred name Distribution).

For gene-as-class concepts, the concept name and preferred name will
usually have the form \'\<*gene symbol*\> Gene\' (*e.g.,* BRCA2_Gene and
BRCA2 Gene, respectively). The HUGO-approved gene symbol will be used in
both the concept name and preferred name. The HUGO-approved gene name
will be used as a FULL_SYN wherein all of the words in the name are
capitalized (e.g., Breast Cancer 2, Early Onset Gene). The HUGO gene
symbol and name listed by the Human Genome Nomenclature Committee
(<http://www.gene.ucl.ac.uk/nomenclature/index.html>) will be used to
ensure the accuracy of these terms. EntrezGene ([Entrez
Gene](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Limits&DB=gene))
will be used as the authority for accepted synonyms (*i.e.*, gene
aliases). Include the bare \'\<*gene symbol*\>\' as a synonym (*e.g.,*
BRCA2).

Note: Wild-type allele concepts have the same synonyms as their
corresponding gene-as-class parents except that '\<*gene symbol*\> wt
Allele' is used (*e.g.*, BRCA2_wt_Allele and BRCA2 wt Allele for the
concept name and preferred name, respectively). Likewise 'wt Allele' is
used in place of 'Gene' for the full name synonym. Finally, the bare
'\<*gene symbol*\>' is not included in wild-type allele concepts as a
synonym.

For genes, do not fill in the \'Gene_Encodes_Product\' property until
after the corresponding protein has been created. Make sure that the
string actually matches the protein\'s preferred name.

Note: This property is currently not being populated nor is it being
removed from concepts which already have this property. The idea is that
when the transition to Protégé occurs, this property will become a role
since this software supports bidirectional relationships.

In cases where the preferred name does not match the concept name it may
not be necessary to have a FULL_SYN that matches the concept name.

Note: This is not necessarily true. The concept name may still be a
valid gene alias. If so, then there should be a synonym which matches
the concept name.

For biological processes, there should only be one process per concept
(e.g., don\'t create \'Growth and Development\'. Instead, create
separate concepts for \'Growth\' and \'Development\').

For header concepts (Classes):

Chemical classification headers based on structure will generally take
the form \'\<*name*\> Compound\'.

Chemical classification headers based on function will generally take
the form \'\<*name*\> Agent\'.

Protein families will generally take the form \'\<*name*\> Protein\'
when the name is a \"function\" (e.g., Enzyme Inhibitor Protein) or the
form \'\<*name*\> Family Protein\' (e.g., FOS Family Protein) when the
name is a header for a group of proteins encoded by a family of genes.

Gene families will generally take the form \'\<*name*\> Gene\' when the
name is a \"function\" (e.g., BCL2 Gene) or the form \'\<*name*\> Family
Gene\' (e.g., Fibroblast Growth Factor Gene Family) when the name is a
header for a family of genes.

All \"text entries\" (e.g., concept name, preferred name, display name,
synonym, definition) must be spell checked in Word before entry in TDE.
They must also be checked so that they don\'t contain the following:
leading or trailing spaces, double spaces between words, non-standard
text characters or line returns. An edit filter should prompt you to
make changes if any of these have been violated, however, you should try
not to rely upon the edit filter.

If you are copying text from web pages, it must first be pasted into
Word before entering this into a concept in TDE. Problems such as line
returns should be readily apparent. The use of Word also facilitates
spell checking of the text.

All definitions (with the exception of general concepts in the Gene and
Gene Product Kinds) should be in the form of a sentence. They should
begin with a capital letter and end with a period. They may not contain
leading spaces or trailing spaces. Any definition you create should
specify NCI as the source. If the definition was \"borrowed\" from some
other source, then this source should receive attribution.

Note: With respect to definitions of general concepts in the Gene and
Gene Product Kinds, a decision was made that the first sentence of the
definition would be a fragment and would not include the concept name.

Properties should only have one value per property. For properties such
as Genbank_Accession_Number or Swiss_Prot, if multiple values are
required they should be separated into multiple properties (e.g.,
instead of \'Swiss_Prot: Q9UBU7, Q9Y2M6\' use \'Swiss_Prot: Q9UBU7\' and
\'Swiss_Prot: Q9Y2M6\').

### Information Sources

[]{#info .anchor}Gene chromosomal locations: [Entrez
Gene](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Limits&DB=gene):
Map Information/Cytogenetic

Gene preferred names and synonyms: [Entrez
Gene](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Limits&DB=gene):
Official Gene Symbol and Alternate Symbols

GenBank accession numbers: [Entrez
Gene](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Limits&DB=gene):
GenBank Sequences

Protein preferred names: [Entrez
Gene](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Limits&DB=gene):
Product and [SwissProt](http://us.expasy.org/cgi-bin/sprot-search-de)

Additional information as needed:

[OMIM](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM)

Etc.

Note: These information sources are currently under review and will
likely undergo some revisions in the near future.

### Appendix

[]{#kinds-1 .anchor}[Kinds]{.underline}:

Abnormal_Cell_Kind

Anatomy_Kind

Biological_Process_Kind

Chemicals_and_Drugs_Kind

Chemotherapy_Regimen_Kind

Clinical_or_Research_Activity_Kind

Diagnostic_and_Prognostic_Factors_Kind

EO_Anatomy_Kind

EO_Findings_and_Disorders_Kind

Equipment_Kind

Findings_Disorders_Kind

Gene_Kind

Gene_Product_Kind

Molecular_Abnormality_Kind

## NCI_Kind

Organism_Kind

Properties_or_Attributes_Kind

Retired_Kind

Technique_Kind

[]{#subsources .anchor}[Allowable term sources]{.underline}:

BioCarta

CDC

CDISC

CTCAE

CTRM

DCP

DTP

FDA

KEGG

NCI

NCI-GLOSS

SEER

[Allowable definition sources]{.underline}:

[]{#defsource-1 .anchor}NCI

NCI-GLOSS

FDA

CTCAE

CDISC

[]{#termtypes .anchor}[Allowable Term Types and their
meanings]{.underline}:

AB Abbreviation

AD Adjectival form (and other parts of grammar)

AQ\* Antiquated term

AQS Antiquated term, used when there is more than one antiquated term
within a concept

BR US brand name

CA2 ISO 3166 Alpha-2 country code

CA3 ISO 3166 Alpha-3 country code

CNU ISO 3166 Numeric country code

CI ISO country code is being deprecated

CN Drug study code

CS US State Department country code

DN Display name

FB Foreign brand name

HD\* Header

PT\* Preferred term

SN Chemical structure name

SY Synonym

\*Notes on Term Type usage: Each concept requires a single term that is
tagged as the NCI preferred term. Usually, the PT term type will be used
for this. However, in special cases, a concept will not have a PT term,
but instead, will have either an HD term or an AQ term. These tags are
considered equivalent to PT by the software. This means that a concept
may have only as single NCI PT, or HD, or AQ term. In those cases where
multiple antiquated terms are needed one should be tagged AQ and the
rest tagged AQS.

### 

### 

#### caDSR Term Addition - Use Cases

[]{#caDSRusecase .anchor}

+---------------------+------------------------------------------------+
| **Case:**           | **Single concept Submission by caDSR Users**   |
+---------------------+------------------------------------------------+
| **Stakeholders:**   | caDSR managers and users                       |
+---------------------+------------------------------------------------+
| **Background:**     | CaDSR team occasionally identifies a term they |
|                     | need to add to caDSR that they cannot find in  |
|                     | NCI EVS or NCI Thesaurus. They can then add    |
|                     | them through the suggest new term mechanism    |
|                     | provided by NCI Metaphrase.                    |
|                     |                                                |
|                     | CaDSR users may not know the appropriate       |
|                     | classification, or semantic type for a         |
|                     | particular term, but may make the request as   |
|                     | if they do know -- for example asking that     |
|                     | something be added as a Pharmacologic          |
|                     | Substance that really isn\'t a Pharmacologic   |
|                     | Substance.                                     |
+---------------------+------------------------------------------------+
| **Starting          | caDSR Users will indicate single or limited    |
| Conditions:**       | numbers of new terms they need through the     |
|                     | Submit New Terms mechanism provided by NCI     |
|                     | Metathesaurus.. Submitter may include caDSR    |
|                     | term name (preferred name), caDSR              |
|                     | abbreviation, classification or \"Semantic     |
|                     | Type\", definition or usage notes. Interface   |
|                     | will also ask for the closest term if there is |
|                     | one.                                           |
+---------------------+------------------------------------------------+
| **Problem:**        | Submitted terms need to be added to NCI        |
|                     | Thesaurus in a timely fashion, but with        |
|                     | careful evaluation because the submitted terms |
|                     | may be inappropriate or contain other errors.  |
|                     | CaDSR needs to be alerted when they have been  |
|                     | added, and when they will be in test and       |
|                     | production.                                    |
+---------------------+------------------------------------------------+
| **Challenging       | Careful evaluation of submitted terms before   |
| Conditions:**       | adding to NCI Thesaurus.                       |
+---------------------+------------------------------------------------+
| **Solution:**       | All submissions are to be evaluated carefully  |
|                     | before they are added to EVS. A process for    |
|                     | adding requested terminology, while detecting  |
|                     | problematic items and promptly reaching joint  |
|                     | EVS - caDSR consensus about how to resolve     |
|                     | problems with requested terms is needed.       |
+---------------------+------------------------------------------------+
| **Actions:**        | **Review of Incoming Terms**:                  |
|                     |                                                |
|                     | Single (limited) submissions received through  |
|                     | the \'Suggest New Term\' mechanism are         |
|                     | supposed to be dealt with within 24 hours. The |
|                     | editor (usually fjr) first makes an effort to  |
|                     | determine if the term is unique or if it is a  |
|                     | logical synonym of an existing concept. If it  |
|                     | is a synonym to an existing concept then this  |
|                     | information, as well as the existing           |
|                     | definitions are returned to the submitter for  |
|                     | approval. Adjustments to the definition may be |
|                     | necessary.                                     |
|                     |                                                |
|                     | In evaluating the term, EVS will start with    |
|                     | the assumption that a requested term           |
|                     | corresponds to common usage or understanding,  |
|                     | and will perform the following checks. Each    |
|                     | requested term will be scrutinized for         |
|                     |                                                |
|                     | -   appropriateness of term: the term and      |
|                     |     classification must be in agreement        |
|                     |                                                |
|                     | -   appropriateness of abbreviation: should    |
|                     |     not cause confusion                        |
|                     |                                                |
|                     | -   appropriateness of classification: the     |
|                     |     term and classification must be in         |
|                     |     agreement                                  |
|                     |                                                |
|                     | -   appropriateness of definition: the         |
|                     |     definition must match the term and         |
|                     |     classification as well as the              |
|                     |     generality/specificity of the term         |
|                     |                                                |
|                     | -   Synonyms will be evaluated carefully as    |
|                     |     inappropriate synonyms will degrade the    |
|                     |     validity of the concept                    |
|                     |                                                |
|                     | EVS will report any discrepancies found to the |
|                     | caDSR curator and the caDSR Project leader.    |
|                     | The EVS discrepancy report will request for    |
|                     | clarification of problematic items and/or      |
|                     | offer suggested ways to deal with problems. It |
|                     | may be necessary to change the term, the       |
|                     | classification or the definition.              |
|                     |                                                |
|                     | EVS will funnel requests for terms through a   |
|                     | domain expert; either they should handle the   |
|                     | whole thing or they should be asked to approve |
|                     | the final result.                              |
|                     |                                                |
|                     | ## Process for Adding/ Returning Terminology   |
|                     |                                                |
|                     | -   EVS will perform a preliminary review of   |
|                     |     the requested terms to detect problematic  |
|                     |     content.                                   |
|                     |                                                |
|                     | -   EVS will determine if the term already     |
|                     |     exists in the EVS.                         |
|                     |                                                |
|                     | -   Problematic content will be pointed out to |
|                     |     caDSR administrator.                       |
|                     |                                                |
|                     | -   Results will be submitted back to caDSR in |
|                     |     the prescribed format. Content will        |
|                     |     include:                                   |
|                     |                                                |
|                     | > CaDSR User Term                              |
|                     | >                                              |
|                     | > NCI Concept Name                             |
|                     | >                                              |
|                     | > NCI Preferred Name                           |
|                     |                                                |
|                     | Concept Type (Generally \"NCI Concept Code\")  |
|                     |                                                |
|                     | Concept Identifier (Generally the actual NCI   |
|                     | concept code)                                  |
|                     |                                                |
|                     | > Definition                                   |
|                     | >                                              |
|                     | > Definition Source                            |
+---------------------+------------------------------------------------+

.

+---------------------+------------------------------------------------+
| **Case:**           | **Bulk load of concepts for use by caDSR       |
|                     | Users**                                        |
+---------------------+------------------------------------------------+
| **Stakeholders:**   | caDSR managers and users                       |
+---------------------+------------------------------------------------+
| **Background:**     | CaDSR team utilizes a procedure to load these  |
|                     | types of items into caDSR from an Excel        |
|                     | spreadsheet. They would like to use this       |
|                     | format for both collecting the terms from      |
|                     | their end users, and as a vehical to request   |
|                     | and collect the related EVS attributes to add  |
|                     | to the spreadsheet which can then be uploaded  |
|                     | to caDSR.                                      |
|                     |                                                |
|                     | CaDSR users may not know the appropriate       |
|                     | classification, or semantic type for a         |
|                     | particular term, but may make the request as   |
|                     | if they do know -- for example asking that     |
|                     | something be added as a Pharmacologic          |
|                     | Substance that really isn\'t a Pharmacologic   |
|                     | Substance.                                     |
+---------------------+------------------------------------------------+
| **Starting          | Excel spreadsheets in Excel Loader format.     |
| Conditions:**       | Submissions may include caDSR term name        |
|                     | (preferred name), caDSR abbreviation,          |
|                     | classification or \"Semantic Type\",           |
|                     | definition or usage notes.                     |
+---------------------+------------------------------------------------+
| **Problem:**        | Submitted terms need to be added to NCI        |
|                     | Thesaurus in a timely fashion, but with        |
|                     | careful evaluation because the submitted terms |
|                     | may be inappropriate or contain other errors.  |
|                     | Concepts need to be returned to caDSR in the   |
|                     | excel loader spreadsheet format.               |
+---------------------+------------------------------------------------+
| **Challenging       | Careful evaluation of submitted terms before   |
| Conditions:**       | adding to NCI Thesaurus.                       |
+---------------------+------------------------------------------------+
| **Solution:**       | All submissions are to be evaluated carefully  |
|                     | before they are added to EVS. A process for    |
|                     | adding requested terminology, while detecting  |
|                     | problematic items and promptly reaching joint  |
|                     | EVS - caDSR consensus about how resolve        |
|                     | problems with requested terms is needed.       |
+---------------------+------------------------------------------------+
| **Actions:**        | **Review of Incoming Terms**:                  |
|                     |                                                |
|                     | All bulk load requests from caDSR will be      |
|                     | funneled thru the EVS point of contact.        |
|                     |                                                |
|                     | Any part of the information supplied in the    |
|                     | bulk submission may be wrong or inappropriate. |
|                     | Therefore EVS will start with the assumption   |
|                     | that a requested term corresponds to common    |
|                     | usage or understanding, and will perform the   |
|                     | following checks. Each requested term will be  |
|                     | scrutinized for                                |
|                     |                                                |
|                     | -   appropriateness of term: the term and      |
|                     |     classification must be in agreement        |
|                     |                                                |
|                     | -   appropriateness of abbreviation: should    |
|                     |     not cause confusion                        |
|                     |                                                |
|                     | -   appropriateness of classification: the     |
|                     |     term and classification must be in         |
|                     |     agreement                                  |
|                     |                                                |
|                     | -   appropriateness of definition: the         |
|                     |     definition must match the term and         |
|                     |     classification as well as the              |
|                     |     generality/specificity of the term         |
|                     |                                                |
|                     | -   Synonyms will be evaluated carefully as    |
|                     |     inappropriate synonyms will degrade the    |
|                     |     validity of the concept                    |
|                     |                                                |
|                     | EVS will report any discrepancies found to the |
|                     | caDSR curator and the caDSR Project leader.    |
|                     | The EVS discrepancy report will request for    |
|                     | clarification of problematic items and/or      |
|                     | offer suggested ways to deal with problems. It |
|                     | may be necessary to change the term, the       |
|                     | classification or the definition.              |
|                     |                                                |
|                     | EVS will requests for terms should be funneled |
|                     | through a domain expert; either they should    |
|                     | handle the whole thing or they should be asked |
|                     | to approve the final result.                   |
|                     |                                                |
|                     | ## Process for Adding/ Returning Terminology   |
|                     |                                                |
|                     | -   EVS will perform a preliminary review of   |
|                     |     the requested terms to detect problematic  |
|                     |     content.                                   |
|                     |                                                |
|                     | -   EVS will usually employ automated lexical  |
|                     |     matching of terms in the bulk load to the  |
|                     |     Thesaurus and Metathesaurus to determine   |
|                     |     if any requested term already exists in    |
|                     |     the EVS.                                   |
|                     |                                                |
|                     | -   Machine matches will be verified by EVS    |
|                     |     staff                                      |
|                     |                                                |
|                     | -   EVS staff will review matches with the     |
|                     |     caDSR curator and the caDSR Project        |
|                     |     Director. Problematic content will be      |
|                     |     pointed out at this time.                  |
|                     |                                                |
|                     | -   If the requested bulk load contains        |
|                     |     numerous problematic items, the load may   |
|                     |     be returned to the requestor for           |
|                     |     modification before loading into EVS.      |
|                     |                                                |
|                     | -   If the requested content is largely free   |
|                     |     of problemantic content, EVS will perform  |
|                     |     bulk loading followed by manual editing of |
|                     |     the Thesaurus to resolve of problematic    |
|                     |     items .                                    |
|                     |                                                |
|                     | -   Results will be submitted back to caDSR in |
|                     |     the Excel Loader format. Content will      |
|                     |     include:                                   |
|                     |                                                |
|                     | > NCI Concept Name                             |
|                     | >                                              |
|                     | > CaDSR Term                                   |
|                     | >                                              |
|                     | > NCI Concept Code                             |
|                     | >                                              |
|                     | > NCI Definition                               |
|                     |                                                |
|                     | **Final Edit Checking**                        |
|                     |                                                |
|                     | caDSR will perform edit checks to identify     |
|                     | errors in the Excel file before terms are      |
|                     | loaded into caDSR.                             |
+---------------------+------------------------------------------------+

### UMLS Semantic Types

# **Entity** 

Physical Object

> Organism
>
> Plant
>
> Alga
>
> Fungus
>
> Virus
>
> Rickettsia or Chlamydia
>
> Bacterium
>
> Archaeon
>
> Animal
>
> Invertebrate
>
> Vertebrate
>
> Amphibian
>
> Bird
>
> Fish
>
> Reptile
>
> Mammal
>
> Human
>
> Anatomical Structure
>
> Embryonic Structure
>
> Anatomical Abnormality
>
> Congenital Abnormality
>
> Acquired Abnormality
>
> Fully Formed Anatomical Structure
>
> Body Part, Organ, or Organ Component
>
> Tissue
>
> Cell
>
> Cell Component
>
> Gene or Genome
>
> Manufactured Object
>
> Medical Device
>
> Drug Delivery Device
>
> Research Device
>
> Clinical Drug
>
> Substance
>
> Chemical
>
> Chemical Viewed Functionally
>
> Pharmacologic Substance
>
> Antibiotic
>
> Biomedical or Dental Material
>
> Biologically Active Substance
>
> Neuroreactive Substance or Biogenic Amine
>
> Hormone
>
> Enzyme
>
> Vitamin
>
> Immunologic Factor
>
> Receptor
>
> Indicator, Reagent, or Diagnostic Aid
>
> Hazardous or Poisonous Substance
>
> Chemical Viewed Structurally
>
> Organic Chemical
>
> Nucleic Acid, Nucleoside, or Nucleotide
>
> Organophosphorus Compound
>
> Amino Acid, Peptide, or Protein
>
> Carbohydrate
>
> Lipid
>
> Steroid
>
> Eicosanoid
>
> Inorganic Chemical
>
> Element, Ion, or Isotope
>
> Body Substance
>
> Food
>
> Conceptual Entity
>
> Idea or Concept
>
> Temporal Concept
>
> Qualitative Concept
>
> Quantitative Concept
>
> Functional Concept
>
> Body System
>
> Spatial Concept
>
> Body Space or Junction
>
> Body Location or Region
>
> Molecular Sequence
>
> Nucleotide Sequence
>
> Amino Acid Sequence
>
> Carbohydrate Sequence
>
> Geographic Area
>
> Finding
>
> Laboratory or Test Result
>
> Sign or Symptom
>
> Organism Attribute
>
> Clinical Attribute
>
> Intellectual Product
>
> Classification
>
> Regulation or Law
>
> Language
>
> Occupation or Discipline
>
> Biomedical Occupation or Discipline
>
> Organization
>
> Health Care Related Organization
>
> Professional Society
>
> Self-help or Relief Organization
>
> Group Attribute
>
> Group
>
> Professional or Occupational Group
>
> Population Group
>
> Family Group
>
> Age Group
>
> Patient or Disabled Group

# **Event** 

Activity

> Behavior
>
> Social Behavior
>
> Individual Behavior
>
> Daily or Recreational Activity
>
> Occupational Activity
>
> Health Care Activity
>
> Laboratory Procedure
>
> Diagnostic Procedure
>
> Therapeutic or Preventive Procedure
>
> Research Activity
>
> Molecular Biology Research Technique
>
> Governmental or Regulatory Activity
>
> Educational Activity
>
> Machine Activity

Phenomenon or Process

> Human-caused Phenomenon or Process
>
> Environmental Effect of Humans
>
> Natural Phenomenon or Process
>
> Biologic Function
>
> Physiologic Function
>
> Organism Function
>
> Mental Process
>
> Organ or Tissue Function
>
> Cell Function
>
> Molecular Function
>
> Genetic Function
>
> Pathologic Function
>
> Disease or Syndrome
>
> Mental or Behavioral Dysfunction
>
> Neoplastic Process
>
> Cell or Molecular Dysfunction
>
> Experimental Model of Disease

Injury or Poisoning

###   {#section-9 .unnumbered}

### UMLS Semantic Types with Definitions

[Back to Semantic Types](#semantic-type)

**Entity**

A broad type for grouping physical and conceptual entities.

[Usage note]{.underline}: Few concepts will be assigned to this broad
type.

**Physical Object**

An object perceptible to the sense of vision or touch.

> **Organism**
>
> Generally, a living individual, including all plants and animals.
>
> **Plant**
>
> An organism having cellulose cell walls, growing by synthesis of
> inorganic substances, generally distinguished by the presence of
> chlorophyll, and lacking the power of locomotion. Plant parts are
> included here as well.
>
> **Alga**
>
> A chiefly aquatic plant that contains chlorophyll, but does not form
> embryos during development and lacks vascular tissue.
>
> **Fungus**
>
> A eukaryotic organism characterized by the absence of chlorophyll and
> the presence of a rigid cell wall. Included here are both slime molds
> and true fungi such as yeasts, molds, mildews, and mushrooms.
>
> **Virus**
>
> An organism consisting of a core of a single nucleic acid enclosed in
> a protective coat of protein. A virus may replicate only inside a host
> living cell. A virus exhibits some but not all of the usual
> characteristics of living things.
>
> **Rickettsia or Chlamydia**
>
> An organism intermediate in size and complexity between a virus and a
> bacterium, and which is parasitic within the cells of insects and
> ticks. Included here are all the chlamydias, also called \"PLT\" for
> psittacosis-lymphogranuloma venereum-trachoma.
>
> **Bacterium**
>
> A small, typically one-celled, prokaryotic micro-organism.
>
> **Archaeon**
>
> A member of one of the three domains of life, formerly called
> Archaebacteria under the taxon Bacteria, but now considered separate
> and distinct. Archaea are characterized by: 1) the presence of
> characteristic tRNAs and ribosomal RNAs; 2) the absence of
> peptidoglycan cell walls; 3) the presence of ether-linked lipids built
> from branched-chain subunits; and 4) their occurrence in unusual
> habitats. While archaea resemble bacteria in morphology and genomic
> organization, they resemble eukarya in their method of genomic
> replication.
>
> **Animal**
>
> An organism with eukaryotic cells, and lacking stiff cell walls,
> plastids and photosynthetic pigments.
>
> **Invertebrate**
>
> An animal which has no spinal column.
>
> **Vertebrate**
>
> An animal which has a spinal column.
>
> [Usage note]{.underline}: Few concepts will be assigned to this broad
> type.
>
> **Amphibian**
>
> A cold-blooded, smooth-skinned vertebrate which characteristically
> hatches as an aquatic larva, breathing by gills. When mature, the
> amphibian breathes with lungs.
>
> **Bird**
>
> A vertebrate having a constant body temperature and characterized by
> the presence of feathers.
>
> **Fish**
>
> A cold-blooded aquatic vertebrate characterized by fins and breathing
> by gills. Included here are fishes having either a bony skeleton, such
> as a perch, or a cartilaginous skeleton, such as a shark, or those
> lacking a jaw, such as a lamprey or hagfish.
>
> **Reptile**
>
> A cold-blooded vertebrate having an external covering of scales or
> horny plates. Reptiles breathe by means of lungs and are generally
> egg-laying.
>
> **Mammal**
>
> A vertebrate having a constant body temperature and characterized by
> the presence of hair, mammary glands and sweat glands.
>
> **Human**
>
> Modern man, the only remaining species of the Homo genus.
>
> [Usage note]{.underline}: If a concept describes a human being from
> the point of view of occupational, family, social status, etc., then a
> type from the \'Group\' hierarchy will be assigned instead.
>
> **Anatomical Structure**
>
> A normal or pathological part of the anatomy or structural
> organization of an organism.
>
> [Usage note]{.underline}: Few concepts will be assigned to this broad
> type.
>
> **Embryonic Structure**
>
> An anatomical structure that exists only before the organism is fully
> formed; in mammals, for example, a structure that exists only prior to
> the birth of the organism. This structure may be normal or abnormal.
>
> **Anatomical Abnormality**
>
> An abnormal structure, or one that is abnormal in size or location.
>
> [Usage note]{.underline}: Use this type if the abnormality in question
> can be either an acquired or congenital abnormality. Neoplasms are not
> included here. These are given the type \'Neoplastic Process\'. If an
> anatomical abnormality has a pathologic manifestation, then it will
> additionally be given the type \'Disease or Syndrome\', (e.g.,
> \"Diabetic Cataract\" will be double-typed for this reason).
>
> **Congenital Abnormality**
>
> An abnormal structure, or one that is abnormal in size or location,
> present at birth or evolving over time as a result of a defect in
> embryogenesis.
>
> [Usage note]{.underline}: If the congenital abnormality involves
> multiple defects then the type \'Disease or Syndrome\' will also be
> assigned.
>
> **Acquired Abnormality**
>
> An abnormal structure, or one that is abnormal in size or location,
> found in or deriving from a previously normal structure. Acquired
> abnormalities are distinguished from diseases even though they may
> result in pathological functioning (e.g., \"hernias incarcerate\").
>
> **Fully Formed Anatomical Structure**
>
> An anatomical structure in a fully formed organism; in mammals, for
> example, a structure in the body after the birth of the organism.
>
> [Usage note]{.underline}: Few concepts will be assigned to this broad
> type.
>
> **Body Part, Organ, or Organ Component**
>
> A collection of cells and tissues which are localized to a specific
> area or combine and carry out one or more specialized functions of an
> organism. This ranges from gross structures to small components of
> complex organs. These structures are relatively localized in
> comparison to tissues.
>
> Usage note: When assigning this type, consider whether \'Body Location
> or Region\' might be the correct choice.
>
> **Tissue**
>
> An aggregation of similarly specialized cells and the associated
> intercellular substance. Tissues are relatively non-localized in
> comparison to body parts, organs or organ components.
>
> **Cell**
>
> The fundamental structural and functional unit of living organisms.
>
> **Cell Component**
>
> A part of a cell or the intercellular matrix, generally visible by
> light microscopy.
>
> **Gene or Genome**
>
> A specific sequence, or in the case of the genome the complete
> sequence, of nucleotides along a molecule of DNA or RNA (in the case
> of some viruses) which represent the functional units of heredity.
>
> **Manufactured Object**
>
> A physical object made by human beings.
>
> **Medical Device**
>
> A manufactured object used primarily in the diagnosis, treatment, or
> prevention of physiologic or anatomic disorders.
>
> Usage note: A medical device may be used for research purposes, but
> since its primary use is for routine medical care, it is distinguished
> from a \'Research Device\' which is used primarily for research
> purposes.
>
> **Research Device**
>
> A manufactured object used primarily in carrying out scientific
> research or experimentation.
>
> [Usage note]{.underline}: A research device is distinguished from a
> \'Medical Device\', which though it may be used for research purposes
> is used primarily for routine medical care.
>
> **Clinical Drug**
>
> A pharmaceutical preparation as produced by the manufacturer. The name
> usually includes the substance, its strength, and the form, but may
> include the substance and only one of the other two items.
>
> [Usage note]{.underline}: Do not double type with Pharmacologic
> Substance, Antibiotic, or other chemical semantic types.
>
> **Substance**
>
> A material with definite or fairly definite chemical composition.
>
> **Chemical**
>
> Compounds or substances of definite molecular composition. Chemicals
> are viewed from two distinct perspectives in the network, functionally
> and structurally. Almost every chemical concept is assigned at least
> two types, generally one from the structure hierarchy and at least one
> from the function hierarchy.
>
> [Usage note]{.underline}: Few concepts will be assigned to this broad
> type.
>
> **Chemical Viewed Functionally**
>
> A chemical viewed from the perspective of its functional
> characteristics or pharmacological activities.
>
> [Usage note]{.underline}: A specific chemical will not be assigned
> here. Groupings of chemicals viewed functionally, such as \"Aerosol
> Propellants\" may appropriately be assigned here. A name that is
> inherently functional, such as \"Food Additives\", will not also be
> assigned a type from the \'Chemical Viewed Structurally\' hierarchy.
>
> **Pharmacologic Substance**
>
> A substance used in the treatment or prevention of pathologic
> disorders. This includes substances that occur naturally in the body
> and are administered therapeutically.
>
> [Usage note]{.underline}: If a substance is both endogenous and
> typically used as a drug, then this type and the type \'Biologically
> Active Substance\' or one of its children are assigned. Body
> substances that are used therapeutically such as whole blood
> preparation, NOS would only receive the type \'Body Substance\'.
> Substances used in the diagnosis or analysis of normal and abnormal
> body functions should be given the type \'Indicator, Reagent, or
> Diagnostic Aid\'.
>
> **Antibiotic**
>
> A pharmacologically active compound produced by growing microorganisms
> which kill or inhibit growth of other microorganisms.
>
> **Biomedical or Dental Material**
>
> A substance used in biomedicine or dentistry predominantly for its
> physical, as opposed to chemical, properties. Included here are
> biocompatible materials, tissue adhesives, bone cements, resins,
> toothpastes, etc.
>
> **Biologically Active Substance**
>
> A generally endogenous substance produced or required by an organism,
> of primary interest because of its role in the biologic functioning of
> the organism that produces it.
>
> [Usage note]{.underline}: If a substance is both endogenous and
> typically used as a drug, then this type, or one of its children, and
> the type \'Pharmacologic Substance\' are assigned.
>
> **Neuroreactive Substance or Biogenic Amine**
>
> An endogenous substance whose activities affect or play an important
> role in the functioning of the nervous system. Included here are
> catecholamines, neuroregulators, neurophysins, etc.
>
> [Usage note]{.underline}: Unlike many of the other types under
> \'Biologically Active Substance\', do not assign this type to drugs
> that are used on the nervous system unless the compound is endogenous.
>
> **Hormone**
>
> In animals, a chemical usually secreted by an endocrine gland whose
> products are released into the circulating fluid. Hormones act as
> chemical messengers and regulate various physiologic processes such as
> growth, reproduction, metabolism, etc. They usually fall into two
> broad classes, steroid hormones and peptide hormones.
>
> [Usage note]{.underline}: Synthetic hormones that are used as drugs
> should receive this type and \'Pharmacologic Substance\'. Plant
> hormones are assigned only to the type \'Pharmacologic Substance\'.
>
> **Enzyme**
>
> A complex chemical, usually a protein, that is produced by living
> cells and which catalyzes specific biochemical reactions. There are
> six main types of enzymes: oxidoreductases, transferases, hydrolases,
> lyases, isomerases, and ligases.
>
> [Usage note]{.underline}: Generally when a concept is assigned to this
> type, it will also be assigned to the type \'Amino Acid, Peptide, or
> Protein\'.
>
> **Vitamin**
>
> A substance, usually an organic chemical complex, present in natural
> products or made synthetically, which is essential in the diet of man
> or other higher animals. Included here are vitamin precursors,
> provitamins, and vitamin supplements.
>
> [Usage note]{.underline}: Essential amino acids are not assigned to
> this type. They will be assigned to the type \'Amino Acid, Peptide, or
> Protein\'. This can be used with \'Pharmacologic Substance\' if the
> compound is being administered therapeutically or if the source has it
> classified as therapeutic (i.e., N\'ICE Sugarless Vitamin C Drops).
>
> **Immunologic Factor**
>
> A biologically active substance whose activities affect or play a role
> in the functioning of the immune system.
>
> [Usage note]{.underline}: Antigens and antibodies are assigned to this
> type. Unlike most biologically active substances, some immunologic
> factors may be exogenous. Vaccines should be given this type and the
> type \'Pharmacologic Substance\'.
>
> **Receptor**
>
> A specific structure or site on the cell surface or within its
> cytoplasm that recognizes and binds with other specific molecules.
> These include the proteins on the surface of an immunocompetent cell
> that binds with antigens, or proteins found on the surface molecules
> that bind with hormones or neurotransmitters and react with other
> molecules that respond in a specific way.
>
> **Indicator, Reagent, or Diagnostic Aid**
>
> A substance primarily of interest for its use in laboratory or
> diagnostic tests and procedures to detect, measure, examine, or
> analyze other chemicals, processes, or conditions.
>
> [Usage note]{.underline}: Radioactive imaging agents should be
> assigned to this type and not to the type \'Pharmacologic Substance\'
> unless they are also being used therapeutically.
>
> **Hazardous or Poisonous Substance**
>
> A substance of concern because of its potentially hazardous or toxic
> effects. This would include most drugs of abuse, as well as agents
> that require special handling because of their toxicity.
>
> [Usage note]{.underline}: Few concepts will be assigned to this broad
> type.
>
> **Chemical Viewed Structurally**
>
> A chemical or chemicals viewed from the perspective of their
> structural characteristics. Included here are concepts which can mean
> either a salt, an ion, or a compound (e.g., \"Bromates\" and
> \"Bromides\").
>
> [Usage note]{.underline}: Concepts are assigned to this type if they
> can be both organic and inorganic (e.g. sulfur compounds). Do not use
> this type if the concept has an important functional aspect (e.g.,
> \"Mylanta Double Strength Liquid\" contains Al(OH)3, Mg(OH)2, and
> simethicone, but would be assigned only to \'Pharmacologic
> Substance\').
>
> **Organic Chemical**
>
> The general class of carbon-containing compounds, usually based on
> carbon chains or rings, and also containing hydrogen (hydrocarbons),
> with or without nitrogen, oxygen, or other elements in which the
> bonding between elements is generally covalent.
>
> [Usage note]{.underline}: Salts of organic chemicals (such as Calcium
> Acetate) would be considered organic chemicals and should not also
> receive the type \'Inorganic Chemical\'.
>
> **Nucleic Acid, Nucleoside, or Nucleotide**
>
> A complex compound of high molecular weight occurring in living cells.
> These are basically of two types, ribonucleic (RNA) and
> deoxyribonucleic (DNA) acids. Nucleic acids are made of nucleotides
> (nitrogen-containing base, a 5-carbon sugar, and one or more phosphate
> group) linked together by a phosphodiester bond between the 5\' and
> 3\' carbon atoms. Nucleosides are compounds composed of a purine or
> pyrimidine base (usually adenine, cytosine, guanine, thymine, uracil)
> linked to either a ribose or a deoxyribose sugar.
>
> [Usage note]{.underline}: If this type has been assigned, the type
> \'Organophosphorus Compound\' will not also be assigned. Naturally
> occurring nucleic acids, nucleosides, or nucleotides will also be
> assigned a type from the \'Biologically Active Substance\' hierarchy.
>
> **Organophosphorus Compound**
>
> An organic compound containing phosphorus as a constituent. Included
> here are organic phosphinic, phosphonic and phosphoric acid
> derivatives and their thiophosphorus counterparts. Excluded are
> phospholipids, sugar phosphates, phosphoproteins, nucleotides, and
> nucleic acids.
>
> **Amino Acid, Peptide, or Protein**
>
> Amino acids and chains of amino acids connected by peptide linkages.
>
> [Usage note]{.underline}: When the concept is both an enzyme and a
> protein, this type and the type \'Enzyme\' will be assigned.
>
> **Carbohydrate**
>
> A generic term that includes monosaccharides, oligosaccharides, and
> polysaccharides as well as substances derived from monosaccharides by
> reduction of the carbonyl group (alditols), by oxidation of one or
> more terminal group to carboxylic acids, or by replacement of one or
> more hydroxy groups by a hydrogen atom, an amino group, a thiol group
> or similar heteroatomic groups. It also includes derivatives of these
> compounds. Included here are sugar phosphates. Excluded are
> glycolipids and glycoproteins.
>
> [Usage note]{.underline}: Glycoproteins should only be typed as
> \'Amino Acid, Peptide, or Protein\'. Sugar phosphates should only be
> typed as \'Carbohydrate\'. Glycolipids should only be typed as
> \'Lipid\'.
>
> **Lipid**
>
> An inclusive group of fat or fat-derived substances that are soluble
> in nonpolar solvents related to fatty acid esters, fatty alcohols,
> sterols, waxes, etc. Included in this group are the saponifiable
> lipids such as glycerides (fats and oils), essential (volatile) oils,
> and phospholipids.
>
> [Usage note]{.underline}: Phospholipids should not also be typed with
> \'Organophosphorus Compound\'. Fatty acids are composed of a chain of
> alkyl groups containing from 4-22 carbon atoms (usually even-numbered)
> and characterized by a terminal carboxyl group.
>
> **Steroid**
>
> One of a group of polycyclic, 17-carbon-atom, fused-ring compounds
> occurring both in natural and synthetic forms. Included here are
> naturally occurring and synthetic steroids, bufanolides, cardanolides,
> homosteroids, norsteroids, and secosteroids.
>
> **Eicosanoid**
>
> An oxygenated metabolite from polyunsaturated 20 carbon fatty acids
> including lipoxygenase and cyclooxygenase products and their synthetic
> analogs. This includes the prostaglandins and thromboxanes.
>
> [Usage note]{.underline}: Naturally occurring eicosanoids will also be
> assigned to a type from the \'Biologically Active Substance\'
> hierarchy. Synthetic eicosanoids will also be assigned to the type
> \'Pharmacologic Substance\'.
>
> **Inorganic Chemical**
>
> Chemical elements and their compounds, excluding the hydrocarbons and
> their derivatives (except carbides, carbonates, cyanides, cyanates and
> carbon disulfide). Generally inorganic compounds contain ionic bonds.
> Included here are inorganic acids and salts, alloys, alkalies, and
> minerals.
>
> **Element, Ion, or Isotope**
>
> One of the 109 presently known fundamental substances that comprise
> all matter at and above the atomic level. This includes elemental
> metals, rare gases, and most abundant naturally occurring radioactive
> elements, as well as the ionic counterparts of elements (NA+, Cl-),
> and the less abundant isotopic forms. This does not include organic
> ions such as iodoacetate to which the type \'Organic Chemical\' is
> assigned.
>
> [Usage note]{.underline}: Group terms such as sulfates would be
> assigned to the type \'Chemical Viewed Structurally\'. Substances such
> as aluminum chloride would be assigned the type \'Inorganic
> Chemical\'. Technetium Tc 99m Aggregated Albumin would not receive
> this type.
>
> **Body Substance**
>
> Extracellular material, or mixtures of cells and extracellular
> material, produced, excreted, or accreted by the body. Included here
> are substances such as saliva, dental enamel, sweat, and gastric acid.
>
> **Food**
>
> Any substance generally containing nutrients, such as carbohydrates,
> proteins, and fats, that can be ingested by a living organism and
> metabolized into energy and body tissue. Some foods are naturally
> occurring, others are either partially or entirely made by humans.
>
> [Usage note]{.underline}: Food additives, food preservatives, and food
> dyes should be given the type \'Chemical Viewed Functionally\'; \"Diet
> Coke\" would be assigned this type.
>
> **Conceptual Entity**
>
> A broad type for grouping abstract entities or concepts.
>
> [Usage note]{.underline}: Few concepts will be assigned to this broad
> type.
>
> **Idea or Concept**
>
> An abstract concept, such as a social, religious or philosophical
> concept.
>
> **Temporal Concept**
>
> A concept which pertains to time or duration.
>
> Usage note: If the concept refers to a phase, stage, cycle, interval,
> period, or rhythm, it is assigned to this type.
>
> **Qualitative Concept**
>
> A concept which is an assessment of some quality, rather than a direct
> measurement.
>
> **Quantitative Concept**
>
> A concept which involves the dimensions, quantity or capacity of
> something using some unit of measure, or which involves the
> quantitative comparison of entities.
>
> [Usage note]{.underline}: If the concept refers to rate or
> distribution, the type \'Temporal Concept\' is not also assigned.
>
> **Functional Concept**
>
> A concept which is of interest because it pertains to the carrying out
> of a process or activity.
>
> **Body System**
>
> A complex of anatomical structures that performs a common function.
>
> **Spatial Concept**
>
> A location, region, or space, generally having definite boundaries.
>
> **Body Space or Junction**
>
> An area enclosed or surrounded by body parts or organs or the place
> where two anatomical structures meet or connect.
>
> **Body Location or Region**
>
> An area, subdivision, or region of the body demarcated for the purpose
> of topographical description.
>
> [Usage note]{.underline}: When assigning this type, consider whether
> \'Body Part, Organ, or Organ Component\' might be the correct choice.
>
> **Molecular Sequence**
>
> A broad type for grouping the collected sequences of amino acids,
> carbohydrates, and nucleotide sequences. Descriptions of these
> sequences are generally reported in the published literature and/or
> are deposited in and maintained by databanks such as GenBank, European
> Molecular Biology Laboratory (EMBL), National Biomedical Research
> Foundation (NBRF), or other sequence repositories.
>
> **Nucleotide Sequence**
>
> The sequence of purines and pyrimidines in nucleic acids and
> polynucleotides. Included here are nucleotide-rich regions, conserved
> sequence, and DNA transforming region.
>
> **Amino Acid Sequence**
>
> The sequence of amino acids as arrayed in chains, sheets, etc., within
> the protein molecule. It is of fundamental importance in determining
> protein structure.
>
> **Carbohydrate Sequence**
>
> The sequence of carbohydrates within polysaccharides, glycoproteins,
> and glycolipids.
>
> **Geographic Area**
>
> A geographic location, generally having definite boundaries.
>
> **Finding**
>
> That which is discovered by direct observation or measurement of an
> organism attribute or condition, including the clinical history of the
> patient. The history of the presence of a disease is a \'Finding\' and
> is distinguished from the disease itself.
>
> [Usage note]{.underline}: Only in rare circumstances will findings be
> double-typed with either \'Pathologic Function\' or \'Anatomical
> Abnormality\'. Most findings will be assigned the types \'Laboratory
> or Test Result\' or \'Sign or Symptom\'. Only those findings that
> relate to patient history or to the determination of a state will be
> assigned the type \'Finding\'.
>
> **Laboratory or Test Result**
>
> The outcome of a specific test to measure an attribute or to determine
> the presence, absence, or degree of a condition.
>
> [Usage note]{.underline}: Laboratory or test results are considered
> inherently quantitative and, thus, are not assigned the additional
> type \'Quantitative Concept\'.
>
> **Sign or Symptom**
>
> An observable manifestation of a disease or condition based on
> clinical judgment, or a manifestation of a disease or condition which
> is experienced by the patient and reported as a subjective
> observation.
>
> **Organism Attribute**
>
> A property of the organism or its major parts.
>
> **Clinical Attribute**
>
> An observable or measurable property or state of an organism of
> clinical interest.
>
> [Usage note]{.underline}: These are the attributes that are being
> evaluated or measured, not the results of the evaluation.
>
> **Intellectual Product**
>
> A conceptual entity resulting from human endeavor. Concepts assigned
> to this type generally refer to information created by humans for some
> purpose.
>
> [Usage note]{.underline}: Concepts referring to theorems, models, and
> systems are assigned here. In some cases, a concept may be assigned to
> both \'Intellectual Product\' and \'Research Activity\'. For example,
> the concept \"Comparative Study\" might be viewed as both an activity
> and the result, or product, of that activity.
>
> **Classification**
>
> A term or system of terms denoting an arrangement by class or
> category.
>
> **Regulation or Law**
>
> An intellectual product resulting from legislative or regulatory
> activity.
>
> **Language**
>
> The system of communication used by a particular nation or people.
>
> **Occupation or Discipline**
>
> A vocation, academic discipline, or field of study, or a subpart of an
> occupation or discipline.
>
> [Usage note]{.underline}: If the concept refers to the individuals who
> have the vocation, the type \'Professional or Occupational Group\'
> will be assigned instead.
>
> **Biomedical Occupation or Discipline**
>
> A vocation, academic discipline, or field of study related to
> biomedicine.
>
> **Organization**
>
> The result of uniting for a common purpose or function. The continued
> existence of an organization is not dependent on any of its members,
> its location, or particular facility. Components or subparts of
> organizations are also included here. Although the names of
> organizations are sometimes used to refer to the buildings in which
> they reside, they are not inherently physical in nature.
>
> **Health Care Related Organization**
>
> An established organization which carries out specific functions
> related to health care delivery or research in the life sciences.
>
> [Usage note]{.underline}: Concepts for health care related
> professional societies are assigned the type \'Professional Society\'.
>
> **Professional Society**
>
> An organization uniting those who have a common vocation or who are
> involved with a common field of study.
>
> **Self-help or Relief Organization**
>
> An organization whose purpose and function is to provide assistance to
> the needy or to offer support to those sharing similar problems.
>
> **Group Attribute**
>
> A conceptual entity which refers to the frequency or distribution of
> certain characteristics or phenomena in certain groups.
>
> **Group**
>
> A conceptual entity referring to the classification of individuals
> according to certain shared characteristics.
>
> [Usage note]{.underline}: Few concepts will be assigned to this broad
> type.
>
> **Professional or Occupational Group**
>
> An individual or individuals classified according to their vocation.
>
> [Usage note]{.underline}: If the concept refers to the discipline or
> vocation itself, rather than to the individuals who have the vocation,
> then the type \'Occupation or Discipline\' will be assigned instead.
>
> **Population Group**
>
> An individual or individuals classified according to their sex, racial
> origin, religion, common place of living, financial or social status,
> or some other cultural or behavioral attribute.
>
> **Family Group**
>
> An individual or individuals classified according to their family
> relationships or relative position in the family unit.
>
> **Age Group**
>
> An individual or individuals classified according to their age.
>
> **Patient or Disabled Group**
>
> An individual or individuals classified according to a disability,
> disease, condition or treatment.

**Event**

A broad type for grouping activities, processes and states.

[Usage note]{.underline}: Few concepts will be assigned to this broad
type.

**Activity**

> An operation or series of operations that an organism or machine
> carries out or participates in.
>
> [Usage note]{.underline}: Few concepts will be assigned to this broad
> type. Wherever possible, one of the more specific types from this
> hierarchy will be chosen. For concepts assigned to this type, the
> focus of interest is on the activity. When the focus of interest is
> the individual or group that is carrying out the activity, then a type
> from the \'Behavior\' hierarchy will be chosen. In general, concepts
> will not receive a type from both the \'Activity\' and the
> \'Behavior\' hierarchies.
>
> **Behavior**
>
> Any of the psycho-social activities of humans or animals that can be
> observed directly by others or can be made systematically observable
> by the use of special strategies.
>
> [Usage Note]{.underline}: Few concepts will be assigned to this broad
> type. For concepts assigned to the \'Behavior\' hierarchy, the focus
> of interest is on the individual or group that is carrying out the
> activity. When the activity is of paramount interest, then a type from
> the \'Activity\' hierarchy will be chosen. In general, concepts will
> not receive a type from both the \'Behavior\' and the \'Activity\'
> hierarchies.
>
> **Social Behavior**
>
> Behavior that is a direct result or function of the interaction of
> humans or animals with their fellows. This includes behavior that may
> be considered anti-social.
>
> [Usage note]{.underline}: \'Social Behavior\' requires the direct
> participation of others and is, thus, distinguished from \'Individual
> Behavior\' which is carried out by an individual, though others may be
> present.
>
> **Individual Behavior**
>
> Behavior exhibited by a human or an animal that is not a direct result
> of interaction with other members of the species, but which may have
> an effect on others.
>
> [Usage note]{.underline}: \'Individual Behavior\' is carried out by an
> individual, though others may be present, and is, thus, distinguished
> from \'Social Behavior\' which requires the direct participation of
> others.
>
> **Daily or Recreational Activity**
>
> An activity carried out for recreation or exercise, or as part of
> daily life.
>
> **Occupational Activity**
>
> An activity carried out as part of an occupation or job.
>
> **Health Care Activity**
>
> An activity of or relating to the practice of medicine or involving
> the care of patients.
>
> **Laboratory Procedure**
>
> A procedure, method, or technique used to determine the composition,
> quantity, or concentration of a specimen, and which is carried out in
> a clinical laboratory. Included here are procedures which measure the
> times and rates of reactions.
>
> **Diagnostic Procedure**
>
> A procedure, method, or technique used to determine the nature or
> identity of a disease or disorder. This excludes procedures which are
> primarily carried out on specimens in a laboratory.
>
> **Therapeutic or Preventive Procedure**
>
> A procedure, method, or technique designed to prevent a disease or a
> disorder, or to improve physical function, or used in the process of
> treating a disease or injury.
>
> **Research Activity**
>
> An activity carried out as part of research or experimentation.
>
> [Usage note]{.underline}: In some cases, a concept may be assigned to
> both this type and the type \'Intellectual Product\'. For example, the
> concept \"Comparative Study\" might be viewed as both an activity and
> the result, or product, of that activity.
>
> **Molecular Biology Research Technique**
>
> Any of the techniques used in the study of or the directed
> modification of the gene complement of a living organism.
>
> **Governmental or Regulatory Activity**
>
> An activity carried out by officially constituted governments, or an
> activity related to the creation or enforcement of the rules or
> regulations governing some field of endeavor.
>
> **Educational Activity**
>
> An activity related to the organization and provision of education.
>
> **Machine Activity**
>
> An activity carried out primarily or exclusively by machines.

**Phenomenon or Process**

A process or state which occurs naturally or as a result of an activity.

> **Human-caused Phenomenon or Process**
>
> A phenomenon or process that is a result of the activities of human
> beings.
>
> [Usage note]{.underline}: If the concept refers to the activity
> itself, rather than the result of that activity, a type from the
> \'Activity\' hierarchy will be assigned instead.
>
> **Environmental Effect of Humans**
>
> A change in the natural environment that is a result of the activities
> of human beings.
>
> **Natural Phenomenon or Process**
>
> A phenomenon or process that occurs irrespective of the activities of
> human beings.
>
> **Biologic Function**
>
> A state, activity or process of the body or one of its systems or
> parts.
>
> [Usage note]{.underline}: Few concepts will be assigned to this broad
> type.
>
> **Physiologic Function**
>
> A normal process, activity, or state of the body.
>
> **Organism Function**
>
> A physiologic function of the organism as a whole, of multiple organ
> systems, or of multiple organs or tissues.
>
> **Mental Process**
>
> A physiologic function involving the mind or cognitive processing.
>
> **Organ or Tissue Function**
>
> A physiologic function of a particular organ, organ system, or tissue.
>
> **Cell Function**
>
> A physiologic function inherent to cells or cell components.
>
> **Molecular Function**
>
> A physiologic function occurring at the molecular level.
>
> **Genetic Function**
>
> Functions of or related to the maintenance, translation or expression
> of the genetic material.
>
> **Pathologic Function**
>
> A disordered process, activity, or state of the organism as a whole,
> of a body system or systems, or of multiple organs or tissues.
> Included here are normal responses to a negative stimulus as well as
> patholologic conditions or states that are less specific than a
> disease. Pathologic functions frequently have systemic effects.
>
> [Usage note]{.underline}: If the process is specific, for example to a
> site or substance, then \'Disease or Syndrome\' will be assigned and
> not \'Pathologic Function\'. For example, \"cerebral anoxia\", \"brain
> edema\", and \"milk hypersensitivity\" will all be assigned to
> \'Disease or Syndrome\' only.
>
> **Disease or Syndrome**
>
> A condition which alters or interferes with a normal process, state,
> or activity of an organism. It is usually characterized by the
> abnormal functioning of one or more of the host\'s systems, parts, or
> organs. Included here is a complex of symptoms descriptive of a
> disorder.
>
> [Usage note]{.underline}: Any specific disease or syndrome that is
> modified by such modifiers as \"acute\", \"prolonged\", etc. will also
> be assigned to this type. If an anatomic abnormality has a pathologic
> manifestation, then it will be given this type as well as a type from
> the \'Anatomical Abnormality\' hierarchy (e.g., \"Diabetic Cataract\"
> will be double-typed for this reason).
>
> **Mental or Behavioral Dysfunction**
>
> A clinically significant dysfunction whose major manifestation is
> behavioral or psychological. These dysfunctions may have identified or
> presumed biological etiologies or manifestations.
>
> **Neoplastic Process**
>
> A new and abnormal growth of tissue in which the growth is
> uncontrolled and progressive. The growths may be malignant or benign.
>
> [Usage note]{.underline}: All neoplasms are assigned to this type. Do
> not also assign a type from the \'Anatomical Abnormality\' hierarchy.
>
> **Cell or Molecular Dysfunction**
>
> A pathologic function inherent to cells, parts of cells, or molecules.
>
> [Usage note]{.underline}: This is not intended to be a repository for
> diseases whose molecular basis has been established.
>
> **Experimental Model of Disease**
>
> A representation in a non-human organism of a human disease for the
> purpose of research into its mechanism or treatment.

**Injury or Poisoning**

A traumatic wound, injury, or poisoning caused by an external agent or
force.

[Usage note]{.underline}: An \`Injury or Poisoning\' is distinguished
from a \'Disease or Syndrome\' that may be a result of prolonged
exposure to toxic materials.

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