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Worm Mine WormBase Workshop International Worm Meeting 2015
1. WormBase Workshop:
2015 International C. elegans Meeting
Tools & Resources
• InterMine / WormMine – Chris Grove
• JBrowse – Scott Cain
• The WormBase Ontology Browser – Raymond Lee
• ParaSite, Ensembl Genomes, and UCSC Assembly
Hub for C. elegans – Kevin Howe/Michael Paulini
• Gene Ontology: annotations and enrichment
tools – Kimberly Van Auken
2. Community Annotation Tools
• Introduction & Overview
– Genetic variations annotation – Mary Ann Tuli
• Contributing & editing gene concise
descriptions – Ranjana Kishore
• Micropublications – Daniela Raciti
WormBase Workshop:
2015 International C. elegans Meeting
3. WormBase Data Mining Options
• WormMine
• Flat files (click “FTP site” under “Downloads”
at bottom of WormBase homepage)
• Website API
• Perl interface
• Bioperl interface to sequence feature
databases
• And more…
7. WormMine: An Overview
• Lists
– Lists of biological
entities
– Constrain queries on
lists
– Compare & contrast,
intersection, union, etc.
• Queries
– Template and custom
queries
– Constrain on biological
entities or lists
• Tables
– Lists and query results
– Sortable,
downloadable
– Export as a
WormMine list
WormMine Entities:
37. Questions?
• E-mail help@wormbase.org anytime, for any
questions!
Thank you!!
Acknowledgements
WormBase Web Development Team:
Todd Harris
Sibyl Gao
Paulo Nuin
Editor's Notes
Welcome to the 2015 International C. elegans Meeting WormBase workshop. The workshop will run for 90 minutes with a total of 8 presentations by WormBase staff. We will first explain how to use new and existing tools and resources such as WormMine, presented by myself, JBrowse presented by Scott Cain, the WormBase Ontology Browser by Raymond Lee, ParaSite, Ensembl Genomes and the UCSC Assembly Hub for C. elegans by Kevin Howe (on Thursday) and Michael Paulini (on Saturday) and Gene Ontology annotations and enrichment tools by Kimberly Van Auken…
…followed by an introduction to our new community annotation tools by Mary Ann Tuli using genetic variation annotation as a use case. We will then hear from Ranjana Kishore who will explain how to contribute and edit gene concise descriptions, and Daniela Raciti who will describe a new process of micropublication to submit expression pattern data
Besides WormMine, WormBase offers a broad range of data mining tools. If you are
conducting an analysis it is always a good idea to check the FTP site which houses
commonly requested precomputed data sets, as well as things like the core genomic
annotation and FASTA sequences. In addition, we provide a number of APIs of both the
website and the underlying databases.
We’ll begin with a quick tutorial of WormMine, the WormBase instance of the InterMine biological data warehouse
At the risk of oversimplification, I’d like to summarize the content and functionality of WormMine by suggesting that there are really only two main types of entities to be concerned with in WormMine: Biological entities, and WormMine entities. There are several biological entities but they can mostly be boiled down to genes, proteins, and their associated attributes. WormMine entities, on the other hand are data structures like Lists, Queries, and results Tables
Gene entities in WormMine contain information such as alleles, allele-phenotypes, genomic coordinates, CDSs and trascripts, Gene Ontology annotations, and expression data such as expression patterns and expression clusters. Protein entities in WormMine contain amino acid sequences, molecular weight, and motifs and domain information
WormMine entities, again, are lists, queries, and tables. Lists are just lists of biological entities which can be used as query constraints and can be used to compare and contrast with other lists to generate intersections, unions, etc. Queries can be custom built from scratch but there are also pre-constructed template queries that can be used and modified for your specific needs. Constraints can be added to queries as single biological entities or as lists of entities. WormMine tables are the way in which lists and query results are displayed to the user; they are sortable and downloadable, and any column of valid entries may be exported as its own list for further use.
To reach WormMine, click on “WormMine” under the Tools menu on the WormBase homepage
Here is the WormMine homepage. There are four aspects of this page I would like to draw your attention to:
First is a brief WormMine tutorial that you can read on our WormBase wiki site by clicking on the “Take a Tour” button
Second, there are two general search boxes to search WormMine for biological entities in the panel to the left and in the header bar at the upper right
Third, there is a tab at the top of the page for WormMine lists and a panel in the center in which you can paste in gene or protein IDs to create a list right away
And fourth, you can reach query templates via the “Templates” tab or the bottom panel of the page, or you can build custom queries using the WormMine QueryBuilder via the QueryBuilder tab
We’ll start by clicking on the Lists tab and exploring WormMine lists
The Lists tab takes you first to the list upload form, where you can paste in a list of biological entities to create a list, or you can upload lists of biological entities from a text file. If we click on the View menu…
We’ll be taken to a list of existing WormMine lists, including lists of phenotypes, expression clusters, and anatomy terms. Typing in the Filter at the top of the page will filter the list of lists to just those that match entered text. You may also compare and contrast lists of the same biological entity type to create a new list that is the union, intersection, or difference between two input lists.
As an example, let’s take a look at the Expression Cluster list
WormMine displays lists in a WormMine Table, with biological entities as rows and attributes as columns. As with other WormMine tables, users may manage columns, add or edit filters on columns, add entities to a list or create a new list, or download the data in a variety of formats.
Also, each column may be sorted or hidden and a column summary displays the number of rows that contain any given entry in descending order.
Coming back to the WormMine homepage, let’s now take a look at WormMine queries. The central, bottom panel of the WormMine homepage consists of several template queries
Template queries are sorted into categories, including queries for genomics, proteins, expression, genetic variations, phenotypes, gene ontology, and reagents
We can also click on the Templates tab to view a list of all existing template queries
As with lists, you can type in the Filter field to narrow down the list of templates to relevant queries. Additionally you can use the Filter drop down list to see only template queries belonging to a particular category.
As an example template query, let’s take a look at the Cell/Tissue expression query template
As with most template queries, selection of this template query takes us first to a query constraint specification page, where we must specify the biological entity or list of entities on which we would like to constrain the query. In this case we’ll be querying for genes that are annotated to be expressed in the C. elegans anchor cell. Once we’ve entered the desired constraint, we can click on “Show Results” to see the query results as a WormMine table.
We can now see an example of a WormMine table as a result of a query, in this case a table listing all of the genes that have been annotated as expressed in the anchor cell.
If we would like to build a custom query, we may do so using the WormMine QueryBuilder, accessible from the QueryBuilder tab visible on the WormMine homepage. We can open the QueryBuilder by specifiying a data type in the panel to the right by clicking on a data type and clicking “Select” or by simply double clicking the data type. Let’s take a look at the Gene QueryBuilder as an example.
Every QueryBuilder page displays a data model browser in the left panel and a query overview showing your current query construction in the right panel
Clicking on the “Show” buttons next to attributes in the model browser will deposit those attributes into the query overview and indicate that these attributes will be displayed in the results table. If we would like to add a constraint, click on the “Constrain” button next to the relevant attribute and you will be directed to…
… a constraint specification page. In this case, we will specify that we want the query to only consider genes for which the gene name contains the letters “C A T”. Clicking on “Add to query” will bring us back…
…to the QueryBuilder with the new constraint indicated in the Query Overview. Now we have a query constructed to return a table of all alleles and observed phenotypes of those alleles for genes that have “C A T” in their name.
Scrolling down to the lower section of the QueryBuilder will reveal the “Columns to Display” summary, where you can remove attribute columns, rearrange the presentation order of columns for the table, and add or edit descriptions of each attribute. Once you’re happy with your query, you can click on “Export XML” to generate an XML version of the query that can then be easily shared with anyone and then imported back into WormMine to replicate the query.
Finally, clicking on “Show Results” will calculate and display the WormMine table with the results of the query.
Back on the QueryBuilder homepage, we can find the link to import a query from XML…
where you can paste in the XML that was exported when we finished building our query. Once we click Submit…
… we arrive at the QueryBuilder with the particular query prepopulated in the query overview panel. We can then make any edits or modifications we see fit for a new, custom query.
That concludes a VERY quick tutorial of WormMine. I’d like to acknowledge Todd Harris, Sibyl Gao, and Paulo Nuin from our web team for development and maintenance of WormMine. If you have any additional questions please don’t hesitate to e-mail help@wormbase.org for any questions. Thank you for your time and attention.
