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The information and links on this page are no longer being updated and a= re provided for reference purposes only.
This page is meant as an explanation of the NCI Prot=C3=A9g=C3=A9 Extens= ions, why they were implemented and what they do.
The Editor's Guide for the most recent version of the NCI Prot=C3=A9g=C3= =A9 extensions can be found on GForge. This provides the= user with instructions on how to edit within the NCI Edit tab, how to do s= earches using the Advanced Search tab, how to handle workflow, pull reports= , etc.
Version 1.2.3.25 is the first public release of the EVS Prot=C3=A9g=C3= =A9 Extensions. There have been multiple revisions released, tested and use= d internally over the past year. The current version is considered stable a= nd reliable and suitable for external release.
These extensions were created in response to a need for an open-source e= diting tool that could be customized to the needs of the EVS content editor= s. In addition, EVS wanted the ability to exchange and share editable conte= nt with external collaborators. The Prot=C3=A9g=C3=A9 editing tool, develop= ed by Stanford, was used as the basis and extended to meet these needs.
The extensions are built on the Prot=C3=A9g=C3=A9 3.1 codebase and utili= ze pellet 1.5. Some improvements to the Prot=C3=A9g=C3=A9 software were req= uired to meet the needs of EVS, but these have already been merged into the= Prot=C3=A9g=C3=A9 trunk. Both Prot=C3=A9g=C3=A9 and Pellet are included wi= thin the download. The Explanation Server was developed in collaboration wi= th Clark & Parsia LLC.
The Prot=C3=A9g=C3=A9 and the extensions are built and expect to run on = Java 1.5.
The EVS Prot=C3=A9g=C3=A9 Extensions are broken into three separate pack= ages. The Explanation Server provides classification and explanation functi= onality. The Prot=C3=A9g=C3=A9 Server provides access to a central editing = project for multiple users. The Prot=C3=A9g=C3=A9 Client is the end-user ap= plication for accessing the Prot=C3=A9g=C3=A9 Server and editing content.= p>
The Explanation Server is used to do classification of the ontology and = provide explanations on demand to the Prot=C3=A9g=C3=A9 Client gui. It runs= directly against the database, independently of the Prot=C3=A9g=C3=A9 Serv= er. The Prot=C3=A9g=C3=A9 Server queries the Explanation Server for informa= tion when needed and controls requests for classification, so multiple clie= nts cannot try and classify at the same time.
The Prot=C3=A9g=C3=A9 Server provides multi-user access to a single onto= logy stored in a database. It coordinates and controls user activities and = resource allocation. It stores a history of user actions for use in trackin= g changes and resolving conflicts. The server also provides a centralized m= eans of enforcing business rules and configurations upon client application= s. EVS has extended the Prot=C3=A9g=C3=A9 Server to allow tracking of workf= low and assigning of editing tasks.
The Prot=C3=A9g=C3=A9 Client is a java-swing based gui used for editing = an ontology. EVS uses the client to connect to the Prot=C3=A9g=C3=A9 Server= application, allowing multiple editors to share the same ontology. The Pro= t=C3=A9g=C3=A9 client can also be used in standalone mode to edit a single = ontology but some of the client-server specific extensions are then disable= d. The client is used in standalone mode by managers to perform Prompt comp= arisons and terminology exports.
The following are EVS business rules that the NCI Edit tab was programme= d to enforce. These rules are a major reason why it was necessary to write = an extension rather than using the default Prot=C3=A9g=C3=A9 editor.
All edits done on the vocabulary are recorded in an audit log in the dat= abase. 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 c= oncept_history and is published on a monthly basis.
The fields in these files are conceptcode|editaction|editdate|referencec= ode.
The record will normally just be a single line and will look like this:<=
br>
C#####|create|dd-mon-yy|(null) or
C#####|modify|dd-mon-yy|(null)
In the particular cases of Split, Merge and Retirement there are multipl= e rows written with reference codes included.
In a split, a single concept is split into two. The original concept sur=
vives and a new concept is generated. Two split records are written for the=
original concept with reference codes for the resulting concepts and a cre=
ate history record is written for the new concept. In the case of C11111 be=
ing 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
In a retirement the concept is moved from its old location in the tree h=
ierarchy 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 mu=
ltiple superconcepts, then a retire record is written for each reference. I=
n the case of retiring concept C11111 which has two superconcepts (C22222 a=
nd C33333), the history will appear as follows:
C11111|retire|dd-mon-yy|C22222
C11111|retire|dd-mon-yy|C33333
In a merge, two concepts are merged into one. One of the two concepts su=
rvives and the other concept is retired.
A merge history record is written for both of the concepts with a referenc=
e code of the surviving concept and a retire record is written for the conc=
ept that retires. In the case of C11111 merging with C22222 and C11111 surv=
iving, the history will appear as follows:
C11111|merge|dd-mon-yy|C11111
C22222|merge|dd-mon-yy|C11111
C22222|retire|dd-mon-yy|(null)
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 ev= s_history is written in real-time, as edits are occurring. The concept_hist= ory is written during the Prompt cycle. The applications allow access to bo= th the Production and QA tiers of both BiomedGT and NCI Thesaurus.