Pathbase

How to use Pathbase

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Contacts and Feedback

Please send an email to mg287@cam.ac.uk for technical questions about this website and to ps@mole.bio.cam.ac.uk for general questions concerning Pathbase.

Instructions for using Pathbase

Pathbase is a Community resource and therefore users are personally responsible for the accuracy of their uploads. Uploaded records will be checked by the Administrator for obvious errors and omissions and the originator will be contacted before the records go live.

We recommend that you use an up-to-date browser version, such as Mozilla to ensure full functionality and optimum display. Not recommended are Netscape 4.x browsers due to various technical diffulties we encountered during testing the interfaces.

Where can I search for images?

Navigate from the index page to:
http://www.pathbase.net/Search_Pathbase/index.php

How do I sign in when I want to upload an image?

Navigate from the index page to:
http://www.pathbase.net//Upload_Images/index.php
Log in with your user ID and password or sign up for a new account.

What information can I submit about each image?

Information is based around each image, which can be standard histopathology or any other kind of image you wish to submit. There are several mandatory fields:


  • Experimental manipulation
  • Strain
  • Genotype status
  • Sex
  • Organism
  • Pathology
  • Tissue
  • Description

And a set of non-mandatory fields
  • Age
  • Cell type
  • Gene
  • Designated mutation name
  • Series number
  • Tbase number
  • Medline number
  • GO ontology terms

These fields are designed for the following types of information:

Experimental manipulation

Describes the experimental manipulation giving rise to the pathology, this may be genetic or some form of experimental treatment.

Strain

A number of commonly used mouse strains are listed under this menu. If the strain you use if not listed please insert the name into the description box which is queried as free text.

Genotype status

Whether your mouse is homozygous, heterozygous, mosaic etc.

Sex

Male, female or 'other'.

Tissue

We have implemented the mouse adult and fetal anatomy ontologies developed jointly by the GXD database and the Jackson Laboratory MGI which can be found here . The list pops up on clicking the MA/Anatomical site box and allows for sequential expansion of the browser or direct searching.

Pathology

As with tissues we have not tried to be encyclopaedic about the types of pathology, but most lesions, including those not associated with cancer, are represented here. The Pathology ontology is organised at the highest level of the hierarchy by the type of pathology. The list pops up as with the tissue controlled vocabulary, and clicking on the term will transfer it to your record. You can search for any term within the list by using CTRL+F. As before, if a specific term is not listed pick that closest to the one you want for the record and include the more detailed one in the description box.
The Pathology ontology can be downloaded from here.

Description

This box is for free text description of the pathology or experimental system and can include any information you like including hypertext links. This box allows very detailed information to be included in the record.  Leaving a box blank in this part of the form is not allowed.


Non-mandatory fields

Age

Age is listed by either Theiler stage (TS) or as broad descriptions of post natal age. Full descriptions of the Theiler stages and their equivalence to human embryos can be found at : http://genex.hgu.mrc.ac.uk/Databases/Anatomy/MAstaging.shtml
Please add the precise age (optional) to the image description box.

Cell type

A broad list of cell types is given here. If your favourite cell is not listed let us know and we can include it. We will implement the CL cell ontology later in 2005

Gene

The appropriate gene symbol or name should be entered here. If in doubt please consult the Mouse genome database
http://www.informatics.jax.org/searches/marker_form.shtml
It is important that the correct symbol is used to allow others to retrieve your record.

Designated allele name

If your mouse has an allele name such as Pudgy(Pu) insert it here. Submissions should use the correct nomenclature rules for naming mouse alleles as determined by the International Committee on Standardized Genetic Nomenclature for Mice. Details can be found here.

Series number

If you upload a set of images from the same tissue or even different tissues on a mouse you can link them together by clicking on the 'create a new series' line below the box. This will bring up a dialog box allowing you to create a new series which will be assigned an identification number, or allow you to add to an existing series.

Tbase number

If your mouse is listed in Tbase insertion of the Tbase identifier here will allow a direct link to the Jackson Laboratories Tbase database from the record.

Medline number

If your mouse has been published or there are relevant papers insert the Medline identifier here and an automatic link will be made to your abstract. If more references are important please insert these in the description box.

GO ontology terms

The Gene Ontology terms for the mutant gene in your mouse. These can be browsed and entered from AMIGO.


In this area of the input form leaving a box blank implies entry not specified.

What kind of image can I submit?

After the record is complete press the submit button. This will open a browser to allow you to select the image you wish to submit and initiate an upload. After the image has been successfully uploaded you get an opportunity to view your record or to return to submit another file. If you have problems with this contact the administrator. We can accept TIFF or JPG files of up to 8MB. Resolution should be about 300 pixels per inch.

Can I expect feedback?

The data sheet includes a field which allows users to feedback by making entries directly on the file. This allow accumulation of comments on specific images which should be helpful to all.

How do I search Pathbase?

Searching Pathbase is effectively the reverse of uploading images. Using the dropdown boxes enter the terms you wish to search. Free text searches can be done in the description box. Click on 'submit' and the matching files will be listed with thumbnails, gene, description and image number. Select the image file you want to examine and click on the thumbnail. This will bring up a data sheet with all of the input data and a field for adding user comments. If the submitter has included a reference to Medline or Tbase this can be automatically retrieved by clicking on the text at the bottom of the datasheet. An additional functionality is an MGD search facility for gene expression pattern and for tumour incidence. This will work in most cases and show you where else this gene is expressed and what the tumour incidence is in this strain of mice. This feature is under development as we continue to consider database interoperability.
Pathbase is currently under continuous development so we would be grateful if you could give us as much feedback as possible on the operation of the database and these instructions on use.

Acknowledging Pathbase and Copyright

This image remains the property of the originating Institution and should not be modified, reproduced or disseminated without the express permission of the submitter.

To cite specific use of this database, use a format similar to that shown below:
Pathbase: A database resource for the histopathology of genetically manipulated mice. World Wide Web (URL: http://www.pathbase.net). [add date (month, yr) when you retrieved data cited].
Individual records should be cited by Record number and original publication if data is published.

Further information:


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