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{scrollbar:icons=false} {pagetreesearch} {section} {column:width=30%} {info:title=To Print the Guide}We recommend you print one wiki page of the guide at a time. To do this, click the printer icon at the top right of the page; then from the browser File menu, choose Print. Printing multiple pages at one time is more complex. For instructions, refer to [WikiTrainFAQsTips:How do I print multiple pages?]. {info} {info:title=Having Trouble Reading the Text?}Resizing the text for any web page is easy. For information on how to do this in your web browser, refer to this {newwindow:W3C tutorial. }http://www.w3.org/WAI/changedesign{newwindow}.{info} {column} {column} Topics in this chapter include: {toc:minLevel=1} {column} {section} h1. Data, Metadata, and Annotations Overview {anchor:Introduction}All of the Gene-Disease and Gene-Compound Cancer Gene Index data, annotations, and metadata are available in the two XML documents and the caBIO interfaces, excluding the caBIO Portlet Templated Search. These data include NCI Thesaurus disease and compound terms, NCI Thesaurus disease and compound concept identifiers, HUGO Gene Symbols, LocusLink Gene Symbols, UniProt Identifiers, the sentences that contained evidence of the gene-disease or gene-compound associations, and the PubMed identifier of the abstract from which each sentence was extracted. The gene-disease and gene-compound data were then annotated by human curators with Evidence Codes, Role Codes, and Role Details; Cell line and Negation Indicators; Sentence and Gene Status Flags; and Comments. For additional information on how these data were collected, validated, and annotated, refer to the [Creation of the Cancer Gene Index|https://wiki.nci.nih.gov/x/DS9yAQ] section. {anchor:Evidence Codes} h1. Evidence Codes Evidence codes qualify the assertions with respect to the association of a gene to a disease or compound term by telling how the assertions were made (for example, through inference or experimental data). The curators may have identified the means by which an assertion using the extracted sentence, alone, or through careful reading of the abstract from which the sentence originated. These codes follow the suggestions of [Karp _et al._|http://www.ncbi.nlm.nih.gov/pubmed/14992503?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1] {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true} for ontologies used in pathway and genome databases. The Evidence Code associated with a specific gene-disease or gene-compound pair is found in the text contents of the [XML|https://wiki.nci.nih.gov/x/8i1yAQ] {{EvidenceCode}} element and is the {{EvidenceCode}} attribute of the caBIO {{Evidence Code class}}, {{
Column

Data, Metadata, and Annotations Overview

Anchor
Introduction
Introduction
All of the Gene-Disease and Gene-Compound Cancer Gene Index data, annotations, and metadata are available in the two XML documents and the caBIO interfaces, excluding the caBIO Portlet Templated Search. These data include NCI Thesaurus disease and compound terms, NCI Thesaurus disease and compound concept identifiers, HUGO Gene Symbols, LocusLink Gene Symbols, UniProt Identifiers, the sentences that contained evidence of the gene-disease or gene-compound associations, and the PubMed identifier of the abstract from which each sentence was extracted. The gene-disease and gene-compound data were then annotated by human curators with Evidence Codes, Role Codes, and Role Details; Cell line and Negation Indicators; Sentence and Gene Status Flags; and Comments.

For additional information on how these data were collected, validated, and annotated, refer to the Creation of the Cancer Gene Index section.

Anchor
Evidence Codes
Evidence Codes

Evidence Codes

Evidence codes qualify the assertions with respect to the association of a gene to a disease or compound term by telling how the assertions were made (for example, through inference or experimental data). The curators may have identified the means by which an assertion using the extracted sentence, alone, or through careful reading of the abstract from which the sentence originated. These codes follow the suggestions of Karp et al.

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for ontologies used in pathway and genome databases. The Evidence Code associated with a specific gene-disease or gene-compound pair is found in the text contents of the XML EvidenceCode element and is the EvidenceCode attribute of the caBIO Evidence Code class,

gov.nih.nci.cabio.domain.EvidenceCode

}}. ||Evidence Code||Description|| |

.

Evidence Code

Description

EV-IC

|

Inferred

by

curator.

An

assertion

was

inferred

by

a

curator

from

relevant

information

such

as

other

assertions

in

a

database.

| |

EV-COMP

|

Inferred

from

computation.

The

evidence

for

an

assertion

comes

from

a

computational

analysis.

The

assertion

itself

might

have

been

made

by

an

author

or

by

a

computer,

that

is,

EV-COMP

does

not

specify

whether

manual

interpretation

of

the

computation

occurred.

| |

EV-COMP-HINF

|

Human

inference.

A

curator

or

author

inferred

this

assertion

after

review

of

one

or

more

possible

types

of

computational

evidence

such

as

sequence

similarity,

recognized

motifs

or

consensus

sequence,

etc.

When

the

inference

was

made

by

a

computer

in

an

automated

fashion,

use

EV-AINF.

| |

EV-COMP-HINF-SIMILAR-TO-CONSENSUS

|

An

author

inferred,

or

reviewed

a

computer

inference

of,

sequence

function

based

on

similarity

to

a

consensus

sequence.

| |

EV-COMP-HINF-POSITIONAL-IDENTIFICATION

|

An

author

inferred,

or

reviewed

a

computer

inference

of,

promoter

position

relative

to

the

-10

and

-35

boxes.

| |

EV-COMP-HINF-FN-FROM-SEQ

|

An

author

inferred,

or

reviewed

a

computer

inference

of,

gene

function

based

on

sequence,

profile,

or

structural

similarity

(as

computed

from

sequence)

to

one

or

more

other

sequences.

| |

EV-COMP-AINF

|

Automated

inference.

A

computer

inferred

this

assertion

through

one

of

many

possible

methods

such

as

sequence

similarity,

recognized

motifs

or

consensus

sequence,

etc.

When

a

person

made

the

inference

from

computational

evidence,

use

EV-HINF.

| |

EV-COMP-AINF-SINGLE-DIRECTON

|

Automated

inference

of

transcription

unit

based

on

single-gene

direction.

Existence

of

a

single-gene

transcription

unit

for

gene

G

is

inferred

computationally

by

the

existence

of

upstream

and

downstream

genes

transcribed

in

the

opposite

direction

of

G.

| |

EV-COMP-AINF-SIMILAR-TO-CONSENSUS

|

A

DNA

sequence

similar

to

previously

known

consensus

sequences

is

computationally

identified.

| |

EV-COMP-AINF-POSITIONAL-IDENTIFICATION

|

Automated

inference

of

promoter

position

relative

to

the

-10

and

-35

boxes.

| |

EV-COMP-AINF-FN-FROM-SEQ

|

Automated

inference

of

function

from

sequence.

A

computer

inferred

a

gene

function

based

on

sequence,

profile,

or

structural

similarity

(as

computed

from

sequence)

to

one

or

more

other

sequences.

| |

EV-AS-TAS

|

Traceable

author

statement.

The

assertion

was

made

in

a

publication

--

– such

as

a

review

--

– that

itself

did

not

describe

an

experiment

supporting

the

assertion.

The

statement

referenced

another

publication

that

supported

the

assertion,

but

it

is

unclear

whether

that

publication

described

an

experiment

that

supported

the

assertion.

| |

EV-AS-NAS

|

Non-traceable

author

statement.

The

assertion

was

made

in

a

publication

such

as

a

review,

without

a

reference

to

a

publication

describing

an

experiment

that

supports

the

assertion.

| |

EV-EXP

|

Inferred

from

experiment.

The

evidence

for

an

assertion

comes

from

a

wet-lab

experiment

of

some

type.

| |

EV-EXP-IPI

|

IPI

inferred

from

physical

interaction

The

assertion

was

inferred

from

a

physical

interaction

such

as

2-hybrid

interactions,

Co-purification,

Co-immunoprecipitation,

Ion/protein

binding

experiments

This

code

covers

physical

interactions

between

the

gene

product

of

interest

and

another

molecule

(or

ion,

or

complex).

For

functions

such

as

protein

binding

or

nucleic

acid

binding,

a

binding

assay

is

simultaneously

IPI

and

IDA;

IDA

is

preferred

because

the

assay

directly

detects

the

binding.

| |

EV-EXP-IDA

|

IDA

inferred

from

direct

assay.

The

assertion

was

inferred

from

a

direct

experimental

assay

such

as

Enzyme

assays,

In

vitro

reconstitution

(for

example,

transcription),

Immunofluorescence,

Cell

fractionation,

etc.

| |

EV-EXP-IDA-UNPURIFIED-PROTEIN

|

Direct

assay

of

unpurified

protein.

Presence

of

a

protein

activity

is

indicated

by

an

assay.

However,

the

precise

identity

of

the

protein

with

that

activity

is

not

established

by

this

experiment

(protein

has

not

been

purified).

| |

EV-EXP-IDA-TRANSCRIPTION-INIT-MAPPING

|

The

transcription

start

site

is

identified

by

primer

extension.

| |

EV-EXP-IDA-TRANSCRIPT-LEN-DETERMINATION

|

The

length

of

the

(transcribed)

RNA

is

experimentally

determined.

The

length

of

the

mRNA

is

compared

with

that

of

the

DNA

sequence

and

by

this

means

the

number

of

genes

transcribed

are

established.

| |

EV-EXP-IDA-RNA-POLYMERASE-FOOTPRINTING

|

The

binding

of

RNA

polymerase

to

a

DNA

region

(the

promoter)

is

shown

by

footprinting.

| |

EV-EXP-IDA-PURIFIED-PROTEIN-MULTSPECIES

|

Protein

purified

from

mixed

culture

or

other

multispecies

environment

(such

as,

infected

plant

or

animal

tissue),

and

activity

measured

through

in

vitro

assay.

| |

EV-EXP-IDA-PURIFIED-PROTEIN

|

Protein

purified

to

homogeneity

from

specific

species

(or

from

heterologous

expression

vector),

and

activity

measured

through

in

vitro

assay.

| |

EV-EXP-IDA-BOUNDARIES-DEFINED

|

Sites

or

genes

bounding

the

transcription

unit

are

experimentally

identified.

Several

possible

cases

exist,

such

as

defining

the

boundaries

of

a

transcription

unit

with

an

experimentally

identified

promoter

and

terminator,

or

with

a

promoter

and

a

downstream

gene

that

is

transcribed

in

the

opposite

direction,

or

with

a

terminator

and

an

upstream

gene

that

is

transcribed

in

the

opposite

direction.

| |

EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS

|

IDA

inferred

from

direct

assay.

The

assertion

was

inferred

from

a

direct

experimental

assay

such

as

Enzyme

assays,

In

vitro

reconstitution

(for

example,

transcription),

Immunofluorescence,

Cell

fractionation.

| |

EV-EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS

|

There

exists

physical

evidence

of

the

binding

of

cellular

extracts

containing

a

regulatory

protein

to

its

DNA

binding

site.

This

can

be

either

by

footprinting

or

mobility

shift

assays.

| |

EV-EXP-IEP

|

IEP

inferred

from

expression

pattern.

The

assertion

was

inferred

from

a

pattern

of

expression

data

such

as

Transcript

levels

(for

example,

Northerns,

microarray

data),

Protein

levels

(for

example,

Western

blots).

| |

EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS

|

The

expression

of

the

gene

is

analyzed

through

a

transcriptional

fusion

(that

is,

lacZ),

and

a

difference

in

expression

levels

is

observed

when

the

regulatory

protein

is

present

(wild

type)

vs

in

its

absence.

Note

that

this

evidence

does

not

eliminate

the

possibility

of

an

indirect

effect

of

the

regulator

on

the

regulated

gene.

| |

EV-EXP-IGI

|

IGI

inferred

from

genetic

interaction.

The

assertion

was

inferred

from

a

genetic

interaction

such

as

"Traditional"

genetic

interactions

such

as

suppressors,

synthetic

lethals,

etc.,

Functional

complementation,

Inference

about

one

gene

drawn

from

the

phenotype

of

a

mutation

in

a

different

gene.

This

category

includes

any

combination

of

alterations

in

the

sequence

(mutation)

or

expression

of

more

than

one

gene/gene

product.

This

category

can

therefore

cover

any

of

the

IMP

experiments

that

are

done

in

a

non-wild-type

background,

although

we

prefer

to

use

it

only

when

all

mutations

are

documented.

| |

EV-EXP-IGI-FUNC-COMPLEMENTATION

|

Protein

activity

inferred

by

isolating

its

gene

and

performing

functional

complementation

of

a

well

characterized

heterologous

mutant

for

the

protein.

| |

EV-EXP-IMP

|

IMP

inferred

from

mutant

phenotype.

The

assertion

was

inferred

from

a

mutant

phenotype

such

as

Any

gene

mutation/knockout,

Overexpression/ectopic

expression

of

wild-type

or

mutant

genes,

Anti-sense

experiments,

RNA

interference

experiments,

Specific

protein

inhibitors,

Complementation.

Inferences

made

from

examining

mutations

or

abnormal

levels

of

only

the

product(s)

of

the

gene

of

interest

are

covered

by

code

EV-IMP

(compare

to

code

EV-IGI).

Use

this

code

for

experiments

that

use

antibodies

or

other

specific

inhibitors

of

RNA

or

protein

activity,

even

though

no

gene

may

be

mutated

(the

rationale

is

that

EV-IMP

is

used

where

an

abnormal

situation

prevails

in

a

cell

or

organism).

| |

EV-EXP-IMP-REACTION-ENHANCED

|

Gene

is

isolated

and

over-expressed,

and

increased

accumulation

of

reaction

product

is

observed.

| |

EV-EXP-IMP-POLAR-MUTATION

|

If

a

mutation

in

a

gene

or

promoter

prevents

expression

of

the

downstream

genes

due

to

a

polar

effect,

the

mutated

gene

is

clearly

part

of

the

transcription

unit.

| |

EV-EXP-IMP-REACTION-BLOCKED

|

Mutant

is

characterized,

and

blocking

of

reaction

is

demonstrated.

| |

EV-EXP-IMP-SITE-MUTATION

|

A

cis-mutation

in

the

DNA

sequence

of

the

transcription-factor

binding

site

interferes

with

the

operation

of

the

regulatory

function.

This

is

considered

strong

evidence

for

the

existence

and

functional

role

of

the

DNA

binding

site.

| |

not_assigned

|

Evidence

Code

was

not

assigned.

| |

based

on

abstract

|

Determinations

of

whether

the

gene-disease

or

gene-compound

association

from

a

sentence

was

factual

based

upon

an

expert's

interpretation

of

the

abstract

from

which

the

sentence

originated.

| | |No Evidence Code was assigned because the sentence did not contain the expected gene-disease or gene-compound association evidence.| {anchor:Role} h1. Role Code and Role Detail Similarities The Cancer Gene Index Role Codes and Role Details are derived from [NCI Role Codes|ftp://ftp1.nci.nih/gov/pub/cacore/EVS/ThesaurusSemantics]. Both describe the semantic associations between gene concept and either a disease or compound concept (that is, concept pairs). Whereas the Evidence Codes describe how the association was inferred or the type of experiment upon which the inference was made, Role Codes and Role Details give information about the actual gene-disease or gene-compound association. Multiple Role Codes and Role Details can be used for the same sentence. {info:title=Note}A concept is the actual compound, disease, or gene to which the various names, acronyms, alternate spellings, and abbreviations refer.{info} {anchor:Role Codes} h2. Role Codes Gene-Disease and Gene-Compound Role Codes most often describe that a gene is associated with a disease or compound (for example, {{

 

No Evidence Code was assigned because the sentence did not contain the expected gene-disease or gene-compound association evidence.

Anchor
Role
Role

Role Code and Role Detail Similarities

The Cancer Gene Index Role Codes and Role Details are derived from NCI Role Codes. Both describe the semantic associations between gene concept and either a disease or compound concept (that is, concept pairs). Whereas the Evidence Codes describe how the association was inferred or the type of experiment upon which the inference was made, Role Codes and Role Details give information about the actual gene-disease or gene-compound association. Multiple Role Codes and Role Details can be used for the same sentence.

Info
titleNote

A concept is the actual compound, disease, or gene to which the various names, acronyms, alternate spellings, and abbreviations refer.

Anchor
Role Codes
Role Codes

Role Codes

Gene-Disease and Gene-Compound Role Codes most often describe that a gene is associated with a disease or compound (for example, GENE_ASSOCIATED_WITH_DISEASE

}}

)

or

how

the

concepts

are

associated

(for

example,

Chemical_or_Drug_Is_Metabolized_By_Enzyme),

but

they

also

may

describe

relevant

features

of

the

role

of

a

particular

gene

(for

example,

{{

GENE_HAS_FUNCTION

}}

).

For

the

former,

the

gene

name,

Role

Code,

and

disease

or

compound

often

can

form

a

sentence,

such

as

"BRCA1

{{

GENE_ASSOCIATED_WITH_DISEASE

}}

BREAST

CANCER."

The

Role

Code

{{

not_assigned

}}

indicates

that

the

curator

did

not

or

could

not

assign

a

specific

code.

The

Role

Code

associated

describing

evidence

of

a

gene-disease

or

gene-compound

pair

is

found

in

the

text

contents

of

the

[

XML

|https://wiki.nci.nih.gov/x/8i1yAQ] {{

PrimaryNCIRoleCode

}}

element

and

is

the

role

attribute

of

the

caBIO

{{

GeneDiseaseAssociation

}}

and

{{

GeneAgentAssociation

}}

classes,

{{

gov.nih.nci.cabio.domain.GeneDiseaseAssociation

}}

and

{{

gov.nih.nci.cabio.domain.GeneAgentAssociation

}}

.

{

Info
:
title
=
Note
}

Although

pharmacological

substances

are

referred

to

as

"compounds"

in

the

Cancer

Gene

Index,

the

NCI

Thesaurus

and

caBIO

use

the

term

"agent."

{info}\\ * {color:blue}*

 

  • Gene-Disease
  • Role
Codes*{color} **
  • Codes
    • Gene_Associated_With_Disease
**
    • Gene_Product_Anormaly_Affects_Pathway
**
    • Gene_Product_Anomaly_Related_To_Gene_Anormaly
**
    • Gene_Product_Encoded_By_Gene
**
    • Gene_Product_Expressed_In_Tissue
**
    • Gene_Product_Has_Associated_Anatomie
**
    • Gene_Product_Has_Biochemical_Function
**
    • Gene_Product_Has_Chemical_Classification
**
    • Gene_Product_Has_Malfunction_Type
**
    • Gene_Product_Has_Organism_Source
**
    • Gene_Product_Has_Structural_Domain_Or_Motif
**
    • Gene_Product_is_Biomarker_of
**
    • Gene_Product_is_Biomarker_Type
**
    • Gene_Product_is_Pathway_Element
**
    • Gene_Product_is_Physical_Part_Of
**
    • Gene_Product_Malfunction_Associated_With_Disease
**
    • Gene_Product_Plays_Role_In_Biological_Process
**
    • Gene_Malfunction_Associated_With_Disease
**
    • Gene_Expressed_In_Tissue
**
    • Gene_Found_In_Organism
**
    • Gene_Has_Anormally
**
    • Gene_Has_Clone
**
    • Gene_Has_Expression_Measurement
**
    • Gene_Has_Function
**
    • Gene_In_Chromosomal_Location
**
    • Gene_is_Biomarker_of
**
    • Gene_Is_Pathway_Element
**
    • Gene_Plays_Role_In_Process
**
    • Disease_Has_Cytogenetic_Abnormality
**
    • Disease_May_Have_Cytogenetic_Abnormality
**
    • Disease_Has_Molecular_Abnormality
**
    • Disease_May_Have_Molecular_Abnormality
\\ * {color:blue}*
  • Gene-Compound
  • Role
Codes*{color} **
  • Codes
    • Chemical_or_Drug_Affects_Cell_Type_or_Tissue
**
    • Chemical_or_Drug_Plays_Role_in_Biological_Process
**
    • Chemical_or_Drug_FDA_Approved_for_Disease
**
    • Chemical_or_Drug_Is_Metabolized_By_Enzyme
**
    • Chemical_or_Drug_Has_Accepted_Therapeutic_Use_For
**
    • Chemical_or_Drug_Has_Study_Therapeutic_Use_For
**
    • Chemical_or_Drug_Has_Mechanism_Of_Action
**
    • Chemical_or_Drug_Affects_Gene_Product
**
    • Chemical_or_Drug_Has_Target_Gene_Product
{anchor:Role Details} h2. Role Details

Anchor
Role Details
Role Details

Role Details

Gene-Disease

and

Gene-Compound

Role

Details

most

often

provide

precise

descriptions

of

the

association

of

a

gene

term

and

a

corresponding

disease

or

compound

term.

These

Details

can

also

describe

relevant

features

of

the

role

of

a

particular

gene

(for

example,

{{

Chemical_or_Drug_Represses_Gene_Product_Expression

}}

).

While

similar

to

Role

Codes,

Role

Details

give

more

specific

semantic

descriptions.

For

example,

a

Role

Detail

for

a

particular

gene-disease

concept

pair

association

may

be

{{

GENE_PRODUCT_UPREGULATED_IN_DISEASE

}}

,

whereas

a

similar

role

code

may

be

{{

GENE_ASSOCIATED_WITH_DISEASE

}}

.

The

Role

Detail

{{

not_assigned

}}

indicates

that

the

curator

did

not

or

could

not

assign

a

specific

semantic

detail.

The

Role

Detail

associated

with

a

specific

gene-disease

or

gene-compound

pair

is

found

in

the

text

contents

of

the

[

XML

|https://wiki.nci.nih.gov/x/8i1yAQ] {{

OtherRole

}}

element

and

is,

like

Role

Codes,

the

role

attribute

of

the

caBIO

{{

GeneDiseaseAssociation

}}

and

{{

GeneAgentAssociation

}}

classes.

* {color:blue}*

  • Gene-Disease
  • Role
Details*{color} **
  • Details
    • Gene_Product_Affects_Disease
**
    • Gene_Product_Affects_Disease_Process
**
    • Gene_Product_Expressed_in_Disease
**
    • Gene_Product_Decreased_in_Disease
**
    • Gene_Product_Increased_in_Disease
**
    • Gene_Product_Level_Changed_in_Disease
**
    • Gene_Expressed_in_Disease
**
    • Gene_Expression_Downregulated_in_Disease
**
    • Gene_Expression_Upregulated_in_Disease
**
    • Gene_Expression_Changed_in_Disease
**
    • Gene_May_Be_Associated_With_Disease
**
    • Gene_Anormaly_has_Disease-Related_Function
**
    • Gene_Anormaly_May_have_Disease-Related_Function
**
    • Gene_Product_Anormaly_has_Disease-Related_Function
**
    • Gene_Product_Anormaly_May_have_Disease-Related_Function
**
    • Gene_has_Therapeutic_Relevance
**
    • Gene_May_have_Therapeutic_Relevance
**
    • Gene_Product_has_Therapeutic_Relevance
**
    • Gene_Product_May_have_Therapeutic_Relevance
* {color:blue}*
  • Gene-Compound
  • Role
Details*{color} **
  • Details
    • Chemical_or_Drug_in_Clinical_Study
**
    • Chemical_or_Drug_May_Affect_Gene_Product
**
    • Chemical_or_Drug_May_Affect_Gene
**
    • Chemical_or_Drug_Affects_Gene
**
    • Chemical_or_Drug_Regulates_Gene
**
    • Chemical_or_Drug_Regulates_Gene_Product
**
    • Chemical_or_Drug_Activates_Gene_Product
**
    • Chemical_or_Drug_Inhibits_Gene_Product
**
    • Chemical_or_Drug_Affects_Gene_Product_Function
**
    • Chemical_or_Drug_Binds_to_Gene_Product
**
    • Chemical_or_Drug_Affects_Expression
**
    • Chemical_or_Drug_Affects_Gene_Expression
**
    • Chemical_or_Drug_Affects_Gene_Product_Expression
**
    • Chemical_or_Drug_Changes_Expression
**
    • Chemical_or_Drug_Induces_Gene_Expression
**
    • Chemical_or_Drug_Induces_Gene_Product_Expression
**
    • Chemical_or_Drug_Regulates_Expression
**
    • Chemical_or_Drug_Represses_Gene_Expression
**
    • Chemical_or_Drug_Represses_Gene_Product_Expression
**
    • Chemical_or_Drug_Mediates_Pathway_Activity
**
    • Chemical_or_Drug_Increases_Pathway_Activity
**
    • Chemical_or_Drug_Decreases_Pathway_Activity
**
    • Chemical_or_Drug_Mediates_Metabolic_Status
**
    • Chemical_or_Drug_Increases_Metabolic_Status
**
    • Chemical_or_Drug_Decreases_Metabolic_Status
**
    • Chemical_or_Drug_Has_Physiologic_Effect
**
    • Gene_Product_Affects_Compound
**
    • Gene_Product_May_Affect_Compound
**
    • Gene_Affects_Compound
**
    • Gene_May_Affect_Compound
**
    • Gene_Product_Antagonizes_Chemical_or_Drug
**
    • Gene_Product_Transports_Compound
**
    • Gene_Anomaly_Effects_Resistance_to_Chemical_or_Drug
**
    • Gene_Product_Anomaly_Effects_Resistance_to_Chemical_or_Drug
**
    • Gene_Anomaly_May_Effect_Resistance_to_Chemical_or_Drug
**
    • Gene_Product_Anomaly_May_Effect_Resistance_to_Chemical_or_Drug
**
    • Gene_is_Associated_with_Resistance_to_Chemical_or_Drug
**
    • Gene_Product_is_Associated_with_Resistance_to_Chemical_or_Drug
**
    • Gene_May_be_Associated_with_Resistance_to_Chemical_or_Drug
**
    • Gene_Product_May_be_Associated_with_Resistance_to_Chemical_or_Drug
{anchor:Indicators} h1. Cell Line and Negation Indicators The binary indicators {{yes}} or {{no}} were set for cell line and negation annotations of each gene-disease and gene-compound association. {anchor:cell line indicators}Cell line indicators denote whether the evidence came from a cell line ({{yes}}) or other source, such a human subject, animal model, or primary cells ({{no}}). The cell line indicator is the text contents of the XML {{CelllineIndicator}} element and the {{celllineStatus}} attribute of the caBIO {{Evidence}} class. {anchor:negation indicators}Negation indicators specify whether the evidence actually described a lack of association between the candidate binary concept pair ({{yes}}), or whether there was a true relationship between them ({{no}}). The curators may have deduced the negation indicator by the extracted sentence, alone, or through careful reading of the abstract from which the sentence originated. Occasionally, the curators did not set a negation indicator ({{-}}). The negation indicator is the text contents of the [XML|https://wiki.nci.nih.gov/x/8i1yAQ] {{NegationIndicator}} element and the {{negationStatus}} attribute of the caBIO {{Evidence}} class. {anchor:status flags} h1. Status Flags The curators set flags to denote the state of annotations of a gene term or of a particular sentence. {anchor:gene status flags} h2. Gene Status Flags Gene Status Flags describe whether annotations for all of the sentences for a given gene term are complete and whether the gene term has been withdrawn from EntrezGene. All low frequency sentence count genes were finished, whereas some [high frequency sentence count genes were not|Creation of the Cancer Gene Index#HFGs]. The status of a specific gene is found in the text contents of the [XML|https://wiki.nci.nih.gov/x/8i1yAQ] {{GeneStatusFlag}} element. {anchor:Gene Status Flags} ||Gene Status Flag||Status Flag Description|| |Finished|All sentences with this gene have been annotated| |New|Not all sentences with this high frequency sentence count gene have been annotated.| |Withdrawn|Gene term has been withdrawn from EntrezGene and, where possible, the term has been mapped to a valid EntrezGene term.| |Entry withdrawn|Gene term has been withdrawn from EntrezGene and, where possible, the term has been mapped to a valid EntrezGene term.| {anchor:sentence status flags} h2. Sentence Status Flags Unlike gene status flags, which can cover many sentences associated with a single gene, Sentence Status Flags describe the curator's findings for a specific sentence. Sentences can be true positives, false positives, unclear, or redundant. The status of a specific gene is found in the text contents of the [XML|https://wiki.nci.nih.gov/x/8i1yAQ] {{SentenceStatusFlag}} element and is the {{sentenceStatus}} attribute of the caBIO {{Evidence}} class. {anchor:Sentence Status Flags} ||Sentence Status Flag||Status Flag Description|| |Finished|Sentence validation and annotation complete| |No_fact|Invalid sentence or false positive| |Unclear|Sentence included both a gene and disease or gene and compound term, but the relationship between the gene-disease or gene-compound pair was not obvious from the sentence.| |Redundant|Identical gene-disease or gene-compound associations were captured from multiple sentences originating from the same abstract.| {anchor:comments} h1. Comments Often, the expert curators made free-text comments on records within the Gene-Disease or Gene-Compound databases. Comments included, but were not limited to, notations of genetic anomalies (for example, loss of heterozygosity, polymorphisms, or aberrant methylation), additional disease information, name of the non-human organism from which the experimental data were collected, information on the cell line or other notable reagents used in the execution of the experiment, and other miscellaneous information. Any comments on a sentence are found in the text contents of the [XML|https://wiki.nci.nih.gov/x/8i1yAQ] {{Comments}} element and the {{comment}} attribute of the caBIO {{Evidence}} class. {column} {section}

Anchor
Indicators
Indicators

Cell Line and Negation Indicators

The binary indicators yes or no were set for cell line and negation annotations of each gene-disease and gene-compound association.

Anchor
cell line indicators
cell line indicators
Cell line indicators denote whether the evidence came from a cell line (yes) or other source, such a human subject, animal model, or primary cells (no). The cell line indicator is the text contents of the XML CelllineIndicator element and the celllineStatus attribute of the caBIO Evidence class.
Anchor
negation indicators
negation indicators
Negation indicators specify whether the evidence actually described a lack of association between the candidate binary concept pair (yes), or whether there was a true relationship between them (no). The curators may have deduced the negation indicator by the extracted sentence, alone, or through careful reading of the abstract from which the sentence originated. Occasionally, the curators did not set a negation indicator (-). The negation indicator is the text contents of the XML NegationIndicator element and the negationStatus attribute of the caBIO Evidence class.

Anchor
status flags
status flags

Status Flags

The curators set flags to denote the state of annotations of a gene term or of a particular sentence.

Anchor
gene status flags
gene status flags

Gene Status Flags

Gene Status Flags describe whether annotations for all of the sentences for a given gene term are complete and whether the gene term has been withdrawn from EntrezGene. All low frequency sentence count genes were finished, whereas some high frequency sentence count genes were not. The status of a specific gene is found in the text contents of the XML GeneStatusFlag element.

Anchor
Gene Status Flags
Gene Status Flags

Gene Status Flag

Status Flag Description

Finished

All sentences with this gene have been annotated

New

Not all sentences with this high frequency sentence count gene have been annotated.

Withdrawn

Gene term has been withdrawn from EntrezGene and, where possible, the term has been mapped to a valid EntrezGene term.

Entry withdrawn

Gene term has been withdrawn from EntrezGene and, where possible, the term has been mapped to a valid EntrezGene term.

Anchor
sentence status flags
sentence status flags

Sentence Status Flags

Unlike gene status flags, which can cover many sentences associated with a single gene, Sentence Status Flags describe the curator's findings for a specific sentence. Sentences can be true positives, false positives, unclear, or redundant. The status of a specific gene is found in the text contents of the XML SentenceStatusFlag element and is the sentenceStatus attribute of the caBIO Evidence class.

Anchor
Sentence Status Flags
Sentence Status Flags

Sentence Status Flag

Status Flag Description

Finished

Sentence validation and annotation complete

No_fact

Invalid sentence or false positive

Unclear

Sentence included both a gene and disease or gene and compound term, but the relationship between the gene-disease or gene-compound pair was not obvious from the sentence.

Redundant

Identical gene-disease or gene-compound associations were captured from multiple sentences originating from the same abstract.

Anchor
comments
comments

Comments

Often, the expert curators made free-text comments on records within the Gene-Disease or Gene-Compound databases. Comments included, but were not limited to, notations of genetic anomalies (for example, loss of heterozygosity, polymorphisms, or aberrant methylation), additional disease information, name of the non-human organism from which the experimental data were collected, information on the cell line or other notable reagents used in the execution of the experiment, and other miscellaneous information. Any comments on a sentence are found in the text contents of the XML Comments element and the comment attribute of the caBIO Evidence class.