PhenoHM Server Help

Index

Home Page
About PhenoHM Server
Overview
Search by MPID or HPID
Search by any other term
Export Cytoscape compatible xgmml files for MP to OMIM mappings
Export Search Results
Source of Mouse Phenotype Data
Source of Human Phenotype Data
Scores in MP-Omim Mapping
Scores in MP-Human Disease Gene Mapping
Glossary
FAQ

About PhenoHM Server

PhenoHM Server (Comparative Phenomics of Human and Mouse): PhenoHM Server is a search based tool to mine Human, Mouse and their Orthologous Phenotypes. The goal of this tool is to allow the user to rapidly obtain a mapping between the human and mouse phenotypes. The tool further aids the user by providing a tree ontology view of the mouse phenotypes. The Human Phenotype records are mapped to the mouse phenotype records based upon the common disease CUI (Concept Unique Identifier) from UMLS (Unified Medical Language System). For this common CUI, the human genes from the human phenotype and the mouse genes from the mouse phenotype are fetched. Based upon these two sets of genes, the ortholog genes are calculated. The OMIM Records and Pubmed IDs from human and the MP terms and descriptions are provided in the results as evidence for the mapped human-mouse phenotypes.

PhenoHM Server Overview

Search Box: It lets a user enter the terms he wishes to search for.

Search Results: This unit provides a summary of the search results produced on hitting a search query. The first row repeats the searched term and provides the number of results searched. The second rows tells where all did the search term hit a match. The summary includes the matched MPID(HPID)s and their corresponding MP(HP) Terms.

Ontology View: This section lists the Mouse(Human) Phenotype Ontology view. The root phenotype terms are colored as blue. The root terms can be expanded to get their children and so on. After a term is searched for, the tree expands to make the matched MPID(HPID)s visible(bolded and in magenta color).

WorkSpace: This section is where the details of the search results are displayed.

Mouse Phenotype Results:

Summary: This section contains three tables: (i) Mapping of Mouse Phenotype to UMLS "Disorder" Concepts (ii) Mapping of Mouse Phenotype to Human OMIM Records (iii) Combined Results for Mapping of Mouse Phenotype to UMLS "Disorder" Concepts and OMIM Records The information represented in each table can be categorized into four parts. The first part represents information about the Mouse Phenotype, that is, the MPTerm, MPDescription and the total number of mouse genes associated with the MPTerm. The second part contains the Score that has been assigned to the mapping by the SKR tool. The third part contains information about the human phenotype, that is, the matched CUI, CUI Term, total number of human genes and the number of OMIM Records linked to the CUI Term. The last part contains information about the Orthologous phenotype, that is, the number of mouse specific genes, human specific genes and orthologous genes.

Detailed Description: Upon clicking the 'MPID' at 'Click Here to view the Complete Map' as shown in above figure a new window showing the detailed description is opened. This page contains a detailed description of the Human-Mouse Phenotype mapping. The summary section has been provided with anchor tags to fetch a detailed information about the summary terms in the Detailed Description section. The detailed information includes a description of MPID and CUI , a description of the human, mouse and orthologous genes,(including geneids, symbols, definition pubmedID and evidence code) and a description of the omim records associated with the human phenotype(including omim ids and their description). A snapshot of the detailed description is shown below:

Human Phenotype Results:

Summary:

The information represented in this table can be categorized into four parts. The first part represents information about the Human Phenotype, that is, the HPID, HPTerm and the total number of HP genes associated with the HPTerm. The second part contains the CUI commonly associated with the Human and Mouse phenotypes mapped. The third part contains information about the mouse phenotype, that is, the matched MPID, MP Term, total number of mouse genes. The last part contains information about the Orthologous phenotype, that is, the number of mouse specific genes, human specific genes and orthologous genes.

Detailed Description: Upon clicking the 'HPID' at 'Click Here to view the Complete Map' as shown in above figure a new window showing the detailed description is opened. This page contains a detailed description of the Human-Mouse Phenotype mapping. The summary section has been provided with anchor tags to fetch a detailed information about the summary terms in the Detailed Description section. The detailed information includes a description of HPID and CUI , a description of the human, mouse and orthologous genes,(including geneids, symbols, definition pubmedID and evidence code) and a description of the omim records associated with the human phenotype(including omim ids and their description). A snapshot of the detailed description is shown below:

Search by MPID or HPID

Search can be done on the basis of MPIDs or HPIDs.
Example for MPID:

Type the MPID in the search box and click the search button.
After the search, the search Results appear in both "Search Results for Mouse Phenotype" and "Search Results for Human Phenotype" sections as follows:
The Mouse and Human Ontology View sections will also expand to show the search results as below:

The search results are highlighted in magenta color:

Example for HPID:

Type the HPID in the search box and click the search button.
After the search, the search Results appear in both "Search Results for Mouse Phenotype" and "Search Results for Human Phenotype" sections as follows:
The Mouse and Human Ontology View sections will also expand to show the search results as below:

The search results are highlighted in magenta color:

Search by any other term

This feature lets one search for the MPID(HPID)s associated with the any searched term. For eg: If the term to be searched is 'cleft palate', the following steps are to be followed:

Type the term to be searched in the search box and hit the search button.
The following results will be shown in the "search Results" section.
The Ontology view will be expanded to show all the MPID(HPID)s which are listed in the Search Results.
In order to get detailed information about any MPID(HPID) in the Search Results, click on it and the Workspace would be populated as follows:

Download Cytoscape compatible xgmml files for MP to OMIM mappings

The MP to OMIM mapping can be viewed in cytoscape through xgmml file formats. These files are created for download by clicking the links (for each score) named "[xgmml]" shown below.

Upon clicking the links, a dialog box opens up prompting the user to save or open the file. User can save the file and view it in Cytoscape software installed locally. The file is named as (MPID)_(Score).xgmml where MPID and score represents the current MPID and score being viewed.

To view the file in Cytoscape user has to follow the instructions below:
(i) Run Cytoscape
(ii) Click 'File'
(iii) Click on 'Import' > 'Network(Multiple File types)'
(iv) Select 'Local' (assuming the file is saved on user's computer locally)
(v) Select the file location
(vi) Click 'Import'
After this user can view/edit the graph in Cytoscape.

Export Search Results

The results of any search can be be exported as an excel file. The export link lies at the top right corner of the Workspace section.

After clicking the export button, you would the following dialog box.

Click on the open or save button accordingly.

Note: Users of Microsoft Office 2007 may encounter a dialog box when opening the excel file saying: 'The file you are trying to open, 'omim_export.jsp.xls' is in a different format than specified by the file extension. Verify that the file is not corrupted and is from a trusted source before opening the file. Do you want to open the file now?' If you see this message, please click 'Yes' to open the file.

Source of Mouse Phenotype Data

The Mouse phenotype information is obtained from the source: ftp://ftp.informatics.jax.org/pub/reports/. The information obtained includes Mouse Gene IDs(MGID); Mouse Phenotype IDs(MPID); Mouse Phenotype Terms,descriptions and synonyms; and mouse genes. Next, a unique list of all the Mouse PhenoType terms, synonyms and descriptions is submitted as a batch Metamap to SKR. SKR processes the input to generate a list of disease CUIs and CUI terms(with a score) associated with the MPIDs.

Source of Human Phenotype Data

The Human Phenotype information is obtained from six sources:UMLS(2007 AA), NCI, OMIM, GENERIF, GAD and RGD. This information includes Human Gene IDs, OMIM Records, Pubmed IDs, associated with disease CUIs along with their terms, descriptions and score.

CRITERIA FOR SCORES IN MP-OMIM MAPPING

Score	Criterion
6	MP Term submitted to NCBI OMIM appears in the Allelic variant and (Clinical Synopsis/Clinical Features)
5	MP Term submitted to NCBI OMIM appears in the Allelic variant
4	MP Term submitted to NCBI OMIM appears in Clinical Synopsis/Clinical Features
3	MP Term submitted to NCBI OMIM appears in Pathogenesis
2	MP Term submitted to NCBI OMIM appears in Genotype/Phenotype Correlations
1	MP Term-OMIM mapping obtained from MGI
0	MP Term submitted to NCBI OMIM appears anywhere else in the OMIM record

CRITERIA FOR SCORES IN MP-HUMAN DISEASE GENE MAPPING

The scores (ranging from 0 to 1000) for MP to UMLS CUI mappings are obtained from the interactive version of MetaMap (SKR) , a text-mining tool which maps free text to UMLS concepts. A score of 1000 indicates a "perfect" match while a score of 700 or less are considered as "weak" matches. For matches that have two or more than two different scores, the highest of the two scores is displayed.

Glossary

Term	Description
UMLS	Unified Medical Language System
CUI	Concept Unique Identifier
MP ID	Mouse Phenotype Identifier
MP Term	Mouse Phenotype Term
HP ID	Human Phenotype Identifier
HP Term	Human Phenotype Term
OMIM ID	Online Mendelian Inheritance in Man Identifier

FAQ

What kind of data retrieval queries are supported by PhenoHM Server?

PhenoHM Server supports search by (a.) Mouse Phenotype ID; (b.) Human Phenotype ID; (c.) any mouse phenotype or human phenotype or disease term ; (d.) any other term (like repair, blood, etc.). The tool also provides advanced search facility wherein (a.) Any specific string of words could be searched for by putting it in quotes, like "adipose tissue";

How to interpret scores in MP-OMIM Mapping?

The following example illustrates on how to interpret the score of MP-OMIM mapping. Search the application for the term 'cataract' by following steps in Search by any other term till we reach the page where MP-OMIM mapping is displayed. The scores for the example term are interpreted as follows: A score of 6 means that the OMIM human gene mapped (RHO) occurs in the allelic variants as well as clinical synopsis of the mapped OMIM ID 180380 as shown below :

The score of 5 means that the OMIM human gene mapped occurs only in the human allelic variants of the mapped OMIM ID 611910 as shown below:

The score of 4 means that the OMIM human gene mapped occurs in the clinical features of the mapped OMIM ID 611391 as shown below:

The score of 3 means that the OMIM human gene mapped occurs in the pathogenesis of the mapped OMIM ID 609026 as shown below:

How can I save a searched result for my later use?

At the top right corner of the WorkSpace, there is a link called 'export'. Click on it to get the searched results in excel format.

What is the meaning of different colors used for naming in the MP(HP) Ontology view?

All the root parent Ids and terms are written in blue color. All the searched MP(HP)IDs and Terms are written in magenta color. Rest of the MP(HP) IDs and terms are written in black color.