FAQ

General Questions

Can I contribute my phenotyping data to EuroPhenome?

Can I become involved in the project?

Common Questions

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

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

How do I find mutants with a particular mouse phenotype?

What ontologies have been used?

How are the ontologies assigned to the data?

What does the annotation pipeline do?

How often is the data uploaded?

What statistics are used?

How can I export data?

What databases does EuroPhenome integrate with?

Answers

Can I contribute my phenotyping data to EuroPhenome?

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 information.

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 than happy to help you become involved.

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

Select the "Baseline Data Viewer" link from the main page. You can then choose a procedure of interest from the dropdown menu and a graphical display of the data for all strains will be displayed. To refine your search by centre, strain, sex or parameter click "Advanced Search Options" and select what you are interested in. You can also view simple descriptive statistics for the strain of choice.

How do I view phenotype data about a particular mutant? back to top

Start typing the gene name into the "Find Gene" box on the home page. This will return a list of genes that match your search. Select the gene you are interested in and a summary of the data we have for that gene will be displayed, as well as links to other related resources. To view the phenotyping data, click on a procedure name (select a different pipeline by clicking on its name). You can access the phenotyping data with finer control by clicking on "Advanced Search Options". This shows you a graphical representation of the data you have requested in comparison to the inbred strain data relevant to that mutant. You can view simple descriptive statistics, as well as the result of statistical significance tests between the mutant and baseline results.

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

Start typing the phenotype into the "Find MP Term" box on the home page. This will return a list of MP terms that match your search that have annotations within EuroPhenome. Select the term you are interested in and a summary of the lines that are annotated to that term, as well as the parameters that generated those annotations are displayed. This information can also be viewed at the level of a whole pipeline, procedure or across all MP terms from the "heat map", or by browsing the MP tree with the "Mine for a Mutant" tool.

If you want to define a more complex phenotypic description based on a number of MP terms click on the "Advanced Search Options" of the phenotype search box. If you select multiple MP terms by typing them into the "Select a phenotypic term" box these terms are added to a single "Complex Phenotype". As they are added the lines that are annotated to all these terms are displayed below (lines that match some of the terms are available by clicking on the "Partial Matches" tab). You can select whether to include (default) or exclude lines that match by clicking on the "logic" condition (AND or NOT). To further refine your search click on "More Options" and you can the select the p value and effect size range you wish to consider.

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.

Where 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 sum 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

EuroPhenome checks for new data nightly. 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.

What statistics are used?back to top

The descriptive statistics for mutant data show the user the mean, SD and SE. The significances of any differences are analysed by rank sum, T-test and, if there are sufficient control animals (>= 120), a reference range comparison.

Rank Sum Test: This test is performed using the Mann-Whitney U test. The significance shown is based on the probability (p) of the observed result occurring if there was no true difference between the two populations tested (the null hypothesis).

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) of the observed result occurring if there was no true difference between the two populations tested (the null hypothesis), assuming normal distribution of data.

Reference Range test: This test is performed by calculating the range of values of the control data set that would exclude the median of the mutant data. If this range is greater than 95% of the actual range of the control data set, the mutant data is considered outside of range.

How can I export data?back to top

Data can be exported from EuroPhenome as CSV files from the Data Viewer. Select the data of interest using the available tools and click the "View Data" link. You can access the annotated data using the biomart. In the future EuroPhenome aims to provide web services as well as other methods for the users to obtain the data computationally. Please contact us if you have any specific requests.

What databases does EuroPhenome integrate with?back to top

Currently EuroPhenome integrates with EUCOMM, Ensembl, MGI, MouseBook, OMIM 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 to request the mutant strains they are interested in. Please contact us if you have any suggestions about datasets that it valuable for EuroPhenome to integrate with.