Europhenome Mouse Phenotyping Resource

Yes you can submit your phenotyping data to EuroPhenome to make it publicly available for database searches, thereby increasing its value, exposure and usefulness. At the moment data is captured as XML files, but at EuroPhenome we are currently working with other centres outside EUMODIC to provide other methods for data submission. Please contact us if you would like to contribute and we will send you the relevant informtion.

Can I become involved in the project?

Yes you can become involved in the project by contributing data or code. EuroPhenome is an open source project, so if you are interested then please contact us and we would be more then happy to help you become involved.

How do I compare the phenotype differences between two wild type strains? back to top

Once you have selected the "Phenome Data Viewer" link from the main page, you can click on the "Inbred Strain Data" radio button at the top of the menu. This will then give you a number of choices to select the relevant inbred strains, the centre's who performed the procedure, the procedure of interest, then the parameters, and then submit the request by clicking on "View Data". This will return a graphical display of all the parameters you have chosen. You can view simple descriptive statistics for the strain of choice.

How do I view phenotype data about a particular mutant or compare results for 2 or more mutants? back to top

Once you have selected the "Phenome Data Viewer" link from the main page, you can click on the "Mutant Data" radio button at the top of the menu. This will then give you a number of choices to select the relevant mutant data. So by holding shift you can select more than one mutant, then choose the procedure and the parameters you are interested in before submitting the query using the "View Data" button. Like the inbred strain viewer this will show you a graphical representation of the data you have suggested in comparison to the inbred strain data relevant to that mutant. You can view simple descriptive statistics, as well as the result of a non-parametric significance test between the mutant and baseline results, matched for centre and strain.

How do I find mutants with a particular mouse phenotype?back to top

You can directly access mutant lines that are potential phenovariants with that phenotype from either the "Mine for Mutant" Tool or the "PhenoMap" tool. The MP Directed Acyclic Graph (DAG) structure can be collapsed into a hierarchy and browsed using the "Mine for Mutant" Tool. Phenotypes can also be retrived by searching by an MP term or synonym. Where mutant lines exhibit an statistically significant phenotype then they are automatically assigned an MP term. The Phenomap illustrates which lines exhibit significant phenodeviance and provides the MP annotation associated with it.

What ontologies have been used?back to top

Ontologies, as used in the biomedical field, can be regarded as a vocabulary of terms where the terms are precisely defined and related to each other in meaningful ways. They are considered a community consensus representation of the specific biological domain they represent. The Mammalian Phenotype (MP) Ontology enables robust annotation of Mammalian phenotypes in the context of mutations and strains that are used as models of human biology and disease (see: The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information). EuroPhenome annotates phenotypes using MP, to provide the unambiguous description of phenotypic observations and allow exact comparisons with other datasets using MP, such as the Mouse Genome Database.

How are the ontologies assigned to the data?back to top

In a process which involved scientific experts in each procedure, most parameters within a procedure are assigned potential MP terms. Quantitative and qualitative (or categorical) parameters are handled differently.

Were quantitative parameters are concerned two potential MP terms are available, one to annotate the increased mutant line phenotype compared to the baseline, and the other to annotate the decreased. So, for example, the "Red Blood Cell count" Haematology parameter (ESLIM_016_001_002) has the MP terms "increased erythrocyte cell number (MP:0003131)" and "decreased erythrocyte cell number (MP:0002875)" associated with it, which are dynamically assigned to a mutant line after statistical comparison with the baseline data. It is worth noting that the search string "red blood cell count" can still be used to retrieve the phenotype data annotated to MP terms involving the string "erythrocyte cell number", since MP provides synonyms for its terms and "increased/decreased red blood cell count" are synonymous with "increased/decreased erythrocyte cell number". Therefore, users searching for phenotypes using familiar terminology will still retrieve MP annotated phenotypes.

Categorical parameters have an MP term associated with each parameter option. So, for example, the "Trunk Curl" Modified SHIRPA parameter (ESLIM_008_001_016) has the options "0=Absent" and "1=Present". The "1=Present" option is associated with the MP term "trunk curl (MP:0001512)" which is assigned to the mutant line if that parameter option is present in statistically significantly increased numbers compared to the background lines.

What does the annotation pipeline do?back to top

The annotation pipeline, compares the mutant cohort data from one parameter in each procedure to the appropriate baseline cohort/s, and calculates a p value using both the t-test and rank sun test. The pipeline then takes the lowest p value from the two tests and if the p is less than 0.05 it identifies the MP term for that parameter and assigns it into the annotation database.

How often is the data uploaded?back to top

The data is uploaded from XML files which are pulled from the phenotyping centres FTP site. Please read this detailed data capture specification for further details. EuroPhenome checks these FTP sites nightly for new data.

What statistics are used?back to top

The overview statistics for mutant data, show the user the mean, SD, SE, significance result from a rank sum and T-test.

Rank Sum Test: This test is performed using the Mann-Whitney U test test. The significance shown is based on the probability (p) that a result that far from expected or more would be achived under the null hypothesis that all samples came from a single distribution.

T-test: This test is performed using the 2 tailed, 2 sample unpaired Student's T-test. The significance shown is based on the probability (p) that a result that far from expected or more would be achived under the null hypothesis that all samples came from a single normal distribution.

How can I export data?back to top

Data can be exported from EuroPhenome as CSV files from the Phenome Data Viewer. In the future EuroPhenome aims to provide web services, a biomart and increased methods for the users to obtain the data

What databases does EuroPhenome integrate with?back to top

Currently EuroPhenome integrates with EUCOMM, Ensembl, MGI, MouseBook and EMMA. EuroPhenome captures the information on clones which have reached GLT (Germ Line Transmisson) from the EUCOMM database and aims to improve links to both the EMMA and MouseBook databases to allow users request the mutant strains they are interested in. EuroPhenome welcomes any suggestions on data sets that would be valuable to integrate with.