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NCI Extensions to Protégé

Anchor
ContentsofthisPage
ContentsofthisPage

Panel
titleContents of this Page
Table of Contents
minLevel2

This page is meant as an explanation of the NCI Protégé Extensions, why they were implemented and what they do.

The Editor's Guide for the most recent version of the NCI Protégé extensions can be found on GForge. This provides the user with instructions on how to edit within the NCI Edit tab, how to do searches using the Advanced Search tab, how to handle workflow, pull reports, etc.

EVS Protégé Extensions Introduction and History

Version 1.2.3.25

...

is

...

the

...

first

...

public

...

release

...

of

...

the

...

EVS

...

Protégé

...

Extensions.

...

There

...

have

...

been

...

multiple

...

revisions

...

released,

...

tested

...

and

...

used

...

internally

...

over

...

the

...

past

...

year.

...

The

...

current

...

version

...

is

...

considered

...

stable

...

and

...

reliable

...

and

...

suitable

...

for

...

external

...

release.

...

These

...

extensions

...

were

...

created

...

in

...

response

...

to

...

a

...

need

...

for

...

an

...

open-source

...

editing

...

tool

...

that

...

could

...

be

...

customized

...

to

...

the

...

needs

...

of

...

the

...

EVS

...

content

...

editors.

...

In

...

addition,

...

EVS

...

wanted

...

the

...

ability

...

to

...

exchange

...

and

...

share

...

editable

...

content

...

with

...

external

...

collaborators.

...

The

...

Protégé

...

editing

...

tool,

...

developed

...

by

...

Stanford,

...

was

...

used

...

as

...

the

...

basis

...

and

...

extended

...

to

...

meet

...

these

...

needs.

...

The

...

extensions

...

are

...

built

...

on

...

the

...

Protégé

...

3.1

...

codebase

...

and

...

utilize

...

pellet

...

1.5.

...

Some

...

improvements

...

to

...

the

...

Protégé

...

software

...

were

...

required

...

to

...

meet

...

the

...

needs

...

of

...

EVS,

...

but

...

these

...

have

...

already

...

been

...

merged

...

into

...

the

...

Protégé

...

trunk.

...

Both

...

Protégé

...

and

...

Pellet

...

are

...

included

...

within

...

the

...

download.

...

The

...

Explanation

...

Server

...

was

...

developed

...

in

...

collaboration

...

with

...

Clark

...

&

...

Parsia

...

LLC.

...

The

...

Protégé

...

and

...

the

...

extensions

...

are

...

built

...

and

...

expect

...

to

...

run

...

on

...

Java

...

1.5.

...

EVS

...

Protégé

...

Extensions

...

packages

...

The

...

EVS

...

Protégé

...

Extensions

...

are

...

broken

...

into

...

three

...

separate

...

packages.

...

The

...

Explanation

...

Server

...

provides

...

classification

...

and

...

explanation

...

functionality.

...

The

...

Protégé

...

Server

...

provides

...

access

...

to

...

a

...

central

...

editing

...

project

...

for

...

multiple

...

users.

...

The

...

Protégé

...

Client

...

is

...

the

...

end-user

...

application

...

for

...

accessing

...

the

...

Protégé

...

Server

...

and

...

editing

...

content.

...

Explanation

...

Server

...

The

...

Explanation

...

Server

...

is

...

used

...

to

...

do

...

classification

...

of

...

the

...

ontology

...

and

...

provide

...

explanations

...

on

...

demand

...

to

...

the

...

Protégé

...

Client

...

gui.

...

It

...

runs

...

directly

...

against

...

the

...

database,

...

independently

...

of

...

the

...

Protégé

...

Server.

...

The

...

Protégé

...

Server

...

queries

...

the

...

Explanation

...

Server

...

for

...

information

...

when

...

needed

...

and

...

controls

...

requests

...

for

...

classification,

...

so

...

multiple

...

clients

...

cannot

...

try

...

and

...

classify

...

at

...

the

...

same

...

time.

...

Protégé

...

Server

...

The

...

Protégé

...

Server

...

provides

...

multi-user

...

access

...

to

...

a

...

single

...

ontology

...

stored

...

in

...

a

...

database.

...

It

...

coordinates

...

and

...

controls

...

user

...

activities

...

and

...

resource

...

allocation.

...

It

...

stores

...

a

...

history

...

of

...

user

...

actions

...

for

...

use

...

in

...

tracking

...

changes

...

and

...

resolving

...

conflicts.

...

The

...

server

...

also

...

provides

...

a

...

centralized

...

means

...

of

...

enforcing

...

business

...

rules

...

and

...

configurations

...

upon

...

client

...

applications.

...

EVS

...

has

...

extended

...

the

...

Protégé

...

Server

...

to

...

allow

...

tracking

...

of

...

workflow

...

and

...

assigning

...

of

...

editing

...

tasks.

...

Protégé Client

The Protégé Client is a java-swing

...

based

...

gui

...

used

...

for

...

editing

...

an

...

ontology.

...

EVS

...

uses

...

the

...

client

...

to

...

connect

...

to

...

the

...

Protégé

...

Server

...

application,

...

allowing

...

multiple

...

editors

...

to

...

share

...

the

...

same

...

ontology.

...

The

...

Protégé

...

client

...

can

...

also

...

be

...

used

...

in

...

standalone

...

mode

...

to

...

edit

...

a

...

single

...

ontology

...

but

...

some

...

of

...

the

...

client-server

...

specific

...

extensions

...

are

...

then

...

disabled.

...

The

...

client

...

is

...

used

...

in

...

standalone

...

mode

...

by

...

managers

...

to

...

perform

...

Prompt

...

comparisons

...

and

...

terminology

...

exports.

...

Protégé

...

Business

...

Rules

...

The

...

following

...

are

...

EVS

...

business

...

rules

...

that

...

the

...

NCI

...

Edit

...

tab

...

was

...

programmed

...

to

...

enforce.

...

These

...

rules

...

are

...

a

...

major

...

reason

...

why

...

it

...

was

...

necessary

...

to

...

write

...

an

...

extension

...

rather

...

than

...

using

...

the

...

default

...

Protégé

...

editor.

...

Rules

...

for

...

Editing

...

  • Each

...

  • concept

...

  • must

...

  • have

...

  • one

...

  • and

...

  • only

...

  • one

...

  • NCI/PT

...

  • Full-Syn

...

  • Each

...

  • concept

...

  • must

...

  • have

...

  • one

...

  • and

...

  • only

...

  • one

...

  • Preferred_Name

...

  • HD,

...

  • AQ

...

  • and

...

  • PT

...

  • are

...

  • equivalent

...

  • Full-Syn

...

  • term

...

  • types.

...

  • (i.e.

...

  • an

...

  • NCI/AQ

...

  • can

...

  • take

...

  • the

...

  • place

...

  • of

...

  • an

...

  • NCI/PT)

...

  • NCI/PT

...

  • value

...

  • must

...

  • match

...

  • the

...

  • Preferred_Name

...

  • Properties

...

  • cannot

...

  • be

...

  • duplicated

...

  • within

...

  • a

...

  • concept

...

  • Roles

...

  • cannot

...

  • be

...

  • duplicated

...

  • within

...

  • a

...

  • concept

...

  • Role

...

  • groups

...

  • cannot

...

  • be

...

  • duplicated

...

  • within

...

  • a

...

  • concept

...

  • Superclasses

...

  • cannot

...

  • be

...

  • duplicated

...

  • within

...

  • a

...

  • concept

...

  • The

...

  • last

...

  • superclass

...

  • of

...

  • a

...

  • concept

...

  • cannot

...

  • be

...

  • deleted

...

  • Cannot

...

  • create

...

  • a

...

  • restriction

...

  • pointed

...

  • at

...

  • a

...

  • retired,

...

  • pre-retired,

...

  • or

...

  • pre-merged

...

  • class

...

  • If

...

  • concept

...

  • has

...

  • Def_Curator

...

  • property

...

  • present,

...

  • only

...

  • authorized

...

  • users

...

  • can

...

  • create,

...

  • modify

...

  • or

...

  • delete

...

  • the

...

  • DEFINITION

...

  • If

...

  • concept

...

  • has

...

  • Def_Curator

...

  • property

...

  • present,

...

  • only

...

  • authorized

...

  • users

...

  • can

...

  • modify

...

  • or

...

  • delete

...

  • the

...

  • Def_Curator

...

  • Def_Curators

...

  • must

...

  • exist

...

  • in

...

  • a

...

  • configuration

...

  • file.

...

  • No

...

  • "dummy"

...

  • Def_Curators

...

  • Each

...

  • DEFINITION

...

  • must

...

  • have

...

  • 1

...

  • review

...

  • date,

...

  • 1

...

  • review

...

  • name,

...

  • 0

...

  • or

...

  • 1

...

  • attributes,

...

  • and

...

  • no

...

  • source

...

  • Only

...

  • single

...

  • spaces

...

  • allowed

...

  • in

...

  • a

...

  • DEFINITION

...

  • unless

...

  • preceeded

...

  • by

...

  • !,

...

  • ?

...

  • or

...

  • .

...

  • No

...

  • leading

...

  • or

...

  • trailing

...

  • spaces

...

  • allowed

...

  • in

...

  • properties

...

  • Only

...

  • single

...

  • spaces

...

  • allowed

...

  • between

...

  • tokens

...

  • in

...

  • properties

...

  • (except

...

  • for

...

  • DEFINITION)

...

  • Properties

...

  • cannot

...

  • include

...

  • the

...

  • characters

...

  • :,

...

  • !,?

...

  • or

...

  • @

...

  • (except

...

  • for

...

  • DEFINITION

...

  • which

...

  • allows

...

  • !

...

  • and

...

  • ?)

...

Retire

  • Pre-retired

...

  • concepts

...

  • are

...

  • retired

...

  • under

...

  • the

...

  • preretired_concepts

...

  • bin

...

  • Pre-retire

...

  • process

...

  • forces

...

  • dependent

...

  • classes

...

  • to

...

  • be

...

  • fixed

...

  • (children

...

  • retreed,

...

  • incoming

...

  • roles

...

  • re-pointed)

...

  • Pre-retire

...

  • concept

...

  • must

...

  • have

...

  • and

...

  • Editor_Note

...

  • added

...

  • explaining

...

  • the

...

  • retirement

...

  • Only

...

  • the

...

  • lead

...

  • editor

...

  • may

...

  • do

...

  • the

...

  • final

...

  • retire

...

  • on

...

  • a

...

  • concept

...

  • Only

...

  • the

...

  • lead

...

  • editor

...

  • may

...

  • edit

...

  • retired

...

  • concepts

...

  • Roles

...

  • in

...

  • the

...

  • retiring

...

  • concept

...

  • converted

...

  • to

...

  • annotation

...

  • properties

...

  • called

...

  • OLD_ROLE

...

  • Retiring

...

  • concept

...

  • deprecated

...

  • using

...

  • owl:deprecatedClass

...

Merge

  • Pre-merge

...

  • retiring

...

  • concepts

...

  • are

...

  • double-treed

...

  • under

...

  • premerged_concepts

...

  • bin

...

  • Pre-merge

...

  • identifying

...

  • properties

...

  • (Merge_From,

...

  • Merge_To)

...

  • are

...

  • added

...

  • to

...

  • the

...

  • surviving

...

  • and

...

  • retiring

...

  • concepts

...

  • Pre-merge

...

  • retiring

...

  • concept

...

  • must

...

  • have

...

  • an

...

  • Editor_Note

...

  • added

...

  • explaining

...

  • the

...

  • merge

...

  • Only

...

  • the

...

  • lead

...

  • editor

...

  • may

...

  • do

...

  • the

...

  • final

...

  • merge

...

  • on

...

  • a

...

  • concept

...

  • Non-redundant

...

  • roles

...

  • and

...

  • properties

...

  • of

...

  • the

...

  • retiring

...

  • concept

...

  • are

...

  • added

...

  • to

...

  • the

...

  • surviving

...

  • concept

...

  • Non-redundant

...

  • incoming

...

  • roles

...

  • pointed

...

  • at

...

  • the

...

  • retiring

...

  • concept

...

  • are

...

  • re-pointed

...

  • at

...

  • the

...

  • surviving

...

  • concept

...

  • Roles

...

  • in

...

  • the

...

  • retiring

...

  • concept

...

  • converted

...

  • to

...

  • annotation

...

  • properties

...

  • called

...

  • OLD_ROLE

...

  • Retiring

...

  • concept

...

  • deprecated

...

  • using

...

  • owl:deprecatedClass

...

History Record Generation

All edits done on the vocabulary are recorded in an audit log in the database. The data recorded includes the username, type of edit, date and time of edit, and reference concepts. This raw audit log is processed to remove any identifying information using Prompt. The scrubbed version is called concept_history and is published on a monthly basis.

The fields in these files are conceptcode|editaction|editdate|referencecode.

...

  • conceptcode

...

  • is

...

  • the

...

  • unique,

...

  • permanent,

...

  • alphanumeric

...

  • identifier

...

  • of

...

  • the

...

  • concept

...

  • editaction

...

  • is

...

  • the

...

  • activity

...

  • being

...

  • recorded

...

  • (create,

...

  • modify,

...

  • split,

...

  • merge,

...

  • retire)

...

  • editdate

...

  • is

...

  • the

...

  • date

...

  • the

...

  • activity

...

  • occurred

...

  • referencecode

...

  • is

...

  • the

...

  • identifier

...

  • for

...

  • a

...

  • concept

...

  • affected

...

  • by

...

  • or

...

  • influencing

...

  • the

...

  • action,

...

  • as

...

  • detailed

...

  • below

...

The

...

record

...

will

...

normally

...

just

...

be

...

a

...

single

...

line

...

and

...

will

...

look

...

like

...

this:

...


C#####|create|dd-mon-yy|(null)

...

or

...


C#####|modify|dd-mon-yy|(null)

...

Special

...

Edits

...

In

...

the

...

particular

...

cases

...

of

...

Split,

...

Merge

...

and

...

Retirement

...

there

...

are

...

multiple

...

rows

...

written

...

with

...

reference

...

codes

...

included.

...

Splits

In a split,

...

a

...

single

...

concept

...

is

...

split

...

into

...

two.

...

The

...

original

...

concept

...

survives

...

and

...

a

...

new

...

concept

...

is

...

generated.

...

Two

...

split

...

records

...

are

...

written

...

for

...

the

...

original

...

concept

...

with

...

reference

...

codes

...

for

...

the

...

resulting

...

concepts

...

and

...

a

...

create

...

history

...

record

...

is

...

written

...

for

...

the

...

new

...

concept.

...

In

...

the

...

case

...

of

...

C11111

...

being

...

split

...

into

...

C11111

...

and

...

C22222

...

the

...

history

...

will

...

appear

...

as

...

follows:

...


C22222|create|dd-mon-yy|(null)

...


C11111|split|dd-mon-yy|C22222

...


C11111|split|dd-mon-yy|C11111

...

Retires

In a retirement the concept is moved from its old location in the tree hierarchy into the Retired_Kind.

...

A

...

retire

...

record

...

is

...

written

...

for

...

the

...

retiring

...

concept

...

with

...

a

...

reference

...

code

...

of

...

the

...

old

...

superconcept.

...

If

...

a

...

concept

...

has

...

multiple

...

superconcepts,

...

then

...

a

...

retire

...

record

...

is

...

written

...

for

...

each

...

reference.

...

In

...

the

...

case

...

of

...

retiring

...

concept

...

C11111

...

which

...

has

...

two

...

superconcepts

...

(C22222

...

and

...

C33333),

...

the

...

history

...

will

...

appear

...

as

...

follows:

...


C11111|retire|dd-mon-yy|C22222

...


C11111|retire|dd-mon-yy|C33333

...

Merges

In a merge,

...

two

...

concepts

...

are

...

merged

...

into

...

one.

...

One

...

of

...

the

...

two

...

concepts

...

survives

...

and

...

the

...

other

...

concept

...

is

...

retired.

...


A

...

merge

...

history

...

record

...

is

...

written

...

for

...

both

...

of

...

the

...

concepts

...

with

...

a

...

reference

...

code

...

of

...

the

...

surviving

...

concept

...

and

...

a

...

retire

...

record

...

is

...

written

...

for

...

the

...

concept

...

that

...

retires.

...

In

...

the

...

case

...

of

...

C11111

...

merging

...

with

...

C22222

...

and

...

C11111

...

surviving,

...

the

...

history

...

will

...

appear

...

as

...

follows:

...


C11111|merge|dd-mon-yy|C11111

...


C22222|merge|dd-mon-yy|C11111

...


C22222|retire|dd-mon-yy|(null)

...

Protégé

...

Editing

...

History

...

Application

...

There

...

are

...

a

...

couple

...

of

...

simple

...

web

...

applications

...

that

...

are

...

made

...

available

...

to

...

allow

...

editors

...

to

...

review

...

the

...

evs_history

...

and

...

concept_history

...

tables.

...

The

...

evs_history

...

is

...

written

...

in

...

real-time,

...

as

...

edits

...

are

...

occurring.

...

The

...

concept_history

...

is

...

written

...

during

...

the

...

Prompt

...

cycle.

...

The

...

applications

...

allow

...

access

...

to

...

both

...

the

...

Production

...

and

...

QA

...

tiers

...

of

...

both

...

BiomedGT

...

and

...

NCI

...

Thesaurus.

...

...

...