FAANGMine v1.2 Documentation¶
FAANGMine is a data mining resource that integrates reference genome assemblies for cattle, horse, pig, sheep, chicken, cat, dog and water buffalo with many other biological data sets. Powered by InterMine, this platform provides access to a number of datasets from a variety of source. It also provides customized bioinformatics tools that researchers can use to create their own custom datasets. FAANGMine is part of FAANGMine.org. The FAANG (Functional Annotation of ANimal Genomes) Consortium is “a coordinated international action to accelerate genome to phenome” and aims to generate comprehensive maps of functional elements in genomes of domesticated animals. FAANGMine will integrate data generated by the FAANG Consortium for animal researchers with or without bioinformatic programming skills to use in their own research projects.
Main site: http://faangmine.org/faangmine
Link to the available datasets in FAANGMine: http://128.206.116.34:8080/faangmine/dataCategories.do
FAANGMine.org is based upon work supported by the National Science Foundation under Award Number 0054449. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. FAANGMine is developed and hosted at the University of Missouri. If you have comments or if you wish to report a problem, please contact the Database Administrator.
Overview of FAANGMine¶
This section provides a brief overview of the layout for FAANGMine.
The navigation panel highlights different functionalities of FAANGMine.
Home - The home page for FAANGMine
MyMine - The MyMine serves as a portal for account management. When logged in to FAANGMine Users can access their saved templates, most recent queries and saved lists.
Templates - List of templates that users can select from based on the nature of their query. Each template is a predefined query with a simple form containing a description of what input is expected and the type of output that will be generated.
Lists - Allows users to upload lists of genes on which they can perform enrichment analyses and export the results. Users that log in to FAANGMine can save their lists for future use.
QueryBuilder - A flexible interface that allows users to create their own custom query template while browing the FAANGMine data models. Queries can be exported in a variety of formats to share with other users.
Regions - The Genomic Region Search tool where users can enter a series of genomic coordinates, specify flanking regions and fetch all features that fall within the given interval. The result can be exported or saved as a list for further analyses.
Data Sources - Provides a summary of all the data loaded into FAANGMine including their sources, associated publications and links to source sites.
Help - Links to the FAANGMine help docs and tutorials
API - Describes the InterMine API that allows users to programmatically access FAANGMine.
Navigation and Searching in FAANGMine¶
There are several ways for users to query FAANGMine.
Quick Search¶
Quick Search allows users to search keywords from any of the FAANGMine datasets. There is a Quick Search box on the FAANGMine home page or a smaller search box in the upper right corner of all pages.
We are currently working to fix our Quick Search tool and hope to have it running again soon.
Quick Search from home page
Quick Search from any page
Quick Searches can be conducted with a number of identifiers including gene names, transcripts, pathways, gene identifiers or organisms. The wildcard character * can be used to retrieve all results that match a particular search query.
For an example, we will use the lysozyme gene LYZ as an example. Enter LYZ in the search box and click Search. The results page is tabulated and displays a summary about your query, as shown below.
Results table for Quick Search with the gene LYZ
Hits are summarized in the box to the left of the results tables and can be filtered based on Category and Organism. Clicking on any of them will filter by the selected category. Note that for results with sequence data available, the sequence can be downloaded in FASTA format by clicking on the FASTA box within the hit Details box. The score column in the result table indicates the similarity of your query to each of the hits. The results page can also be converted to a list (and saved if users are logged in). To enable this feature click on Gene in the Hits by Category then click on C. lupus familiaris in Hits by Organism.
Results table for Quick Search with the gene LYZ filtered by gene then by organism ..
After the table has been filtered for gene and organism, checkboxes will be available for users to select genes they would like to add to their list. Once the genes are selected, click on CREATE LIST. See the lists section for more detail on creating and saving lists.
Templates¶
Templates or predefined queries are another search method within FAANGMine. Popular templates are displayed on the home page, grouped by category (e.g., Genes, Proteins, Interactions) and the complete list can be seen by clicking the Templates menu tab.
Popular templates
Full list of templates on Templates page
As an example, the Gene -> Homologues template queries FAANGMine to retrieves all homologue for a given gene. Here, we will do a search for the gene GSTM1.
Example: Gene –> Homologue
The results page displays all of the homologues for that query gene. When logged in to FAANGMine, users can save their results as a list for further analyses by clicking on the Save as List button above the results table then choosing columns to save in their list. See the lists section for more detail on creating and saving lists. Note the “Trail: Query” text at the upper left of the results table. Clicking on the “Query” link will bring you back to the query that generated the table to allow for edits without having to start with a new template.
Example: Gene –> Homologue template search results, identifier for Gene GSTM1
Generate query code¶
The code for each template query can be retrieved by clicking on the arrow next to Generate Python Code and choosing the desired language from the pull-down menu. The language options are Python, Perl, Java, Ruby, JavaScript, and XML.
Options for generating code from template query
Download results¶
The search results from a template query can be downloaded by clicking the Export button above the table and choosing the desired format from the pull-down menu to the right of the File name field. Available formats are tab-separated values, comma-separated values, XML, and JSON. When the results contain genomic features, they may also be downloaded in FASTA, GFF3, or BED format. Other options may be specified in the submenu to the left of the download box. By default, all rows and all columns are downloaded, but individual columns may be included or excluded by clicking on the toggles next to the column headers in the All Columns submenu. The number of rows and row offset are set in the All Rows submenu. Download the results as a compressed file by choosing GZIP or ZIP format in the Compression submenu (default is No Compression). Column headers are not added by default but may be included under the Column Headers submenu. Finally, the Preview submenu displays the first three rows of the file to be downloaded so that the desired format and options may be finalized before beginning the download. When ready, click the Download file button to download the results.
Options for downloading results from template query
Customize output and manage columns¶
To customize the results table layout, click the Manage Columns button. This allows users to rearrange, remove or order columns. Filters can be edited by clicking the Manage Filters button. To specify the entity relationships within the query and change the way the results are presented in the table, click Manage Relationships. Clicking on the Manage Relationships option bring also brings up a blue information panel (“What does this do?”) that provides more detailed information.
Options for customizing the results of a template query.
To further manage column data, each column has a set of icons in its header. Mousing over any icon will reveal what it does. The sort icon resembles two triangles and allows you to sort a column in either direction (ascending/descending; a->z, z->a). To delete any column from your table, click on the “x” icon. Alternatively, the three dots “…” can be selected to “Toggle column visibility” and hide the column. Once hidden, the icon turns into a double arrow that can be selected to expand the column into its original form. The next icon resembling a funnel can be selected to edit or remove any currently active filters. A summary of the data within a column can be viewed by clicking on the icon that resembles a graph. The data within each summary can be selected for further filtering or downloading.
Column header icons available to edit the results of a template query.
Optional filters¶
Some templates have optional filters that are disabled by default. For the Gene –> Homologue query, there is an optional filter to specify the organism used in the query. To enable the filter, click ON below the Organism > Short Name label.
Using the optional organism filter in the Gene –> Homologue query template.
QueryBuilder¶
The provided templates are suitable for many different types of searches, new queries may be built from scratch using the QueryBuilder. The possibilities of queries using the QueryBuilder are endless. The output may be formatted exactly as desired, and the query constraints may be chosen to perform complex search operations.
To begin, select a Data Type. For example, select Gene as a Data Type then click the Select button to be taken to the Model browser.
Selecting data type as Gene in QueryBuilder.
Model browser¶
After selecting a data type, the Model builder appears displaying the attributes for the chosen feature class Gene.
First lets select Gene as a Data Type in the QueryBuilder. Then click on Select. This will take you to a Model browser where you can select the attributes for the feature class ‘Gene’, which you would want to be shown in your results.
Model browser with “Gene” selected as the data type.
QueryBuilder Examples¶
The following three examples provide details as to how to use the QueryBuilder using “Gene” as the selected data type.
Example 1: Querying for protein coding genes¶
In the Model browser, click Show next to Biotype, Gene ID and Symbol, which will add these fields to the query. Notice that these two fields appear below the data type Gene in the Query Overview section.
Model browser with “Gene” selected as the data type.
Example 1, Step 1: Select fileds to be added to the query
Then click Constrain next to Biotype. The first drop-down menu defaults to = (equals sign). In the second drop-down menu, select Protein Coding, then click the Add to query button. This adds a constraint to the query to search only for protein coding genes. Notice that the Query Overview section now shows “Biotype = Protein Coding”. Also, two types of icons appear next to the attributes. Clicking on the red “X” icon next to an attribute will remove that field or constraint from the query. Clicking on the blue pencil icon next to a constraint brings up the constraint editing window where changes may be made to the query filters.
Example 1, Step 2 Adding a constraint to the query on Biotype.
Lastly, click on Show Results above the Model Browser. The resulting table contains all protein coding genes in the database, with Gene ID, Gene Symbol and Gene Biotype as the table columns. Because the Biotypes should all be the same (protein coding), that column can be deleted by clicking the “x” above it. Alternatively, the three dots “…” can be selected to “Toggle column visibility” and hide the column. See the Customize output and manage columns section to review ways to manage column data.
Example 1, Step 3 Display query results.
Example 2: Querying for protein coding genes on a particuler chromosome¶
Users can customize the previously run query by adding another constraint for Chromosome. Note the “Trail: Query” text at the upper left of the results table. Clicking on the “Query” link will bring you back to the query that generated the table to allow for edits without having to build a new query. In the Model browser, click on the “+” (plus sign) next to the Chromosome feature class to display its attributes.
Example 2, Step 1 View attributes of Chromosome feature class
Next click on Constrain next to the Chromosome ID attribute and in the text box of the pop-up window select “=” (equals). Enter 18 for chromosome number 18then click on Add to Query, which adds the additional constraint to the query. Just clicking chromosome 18 will bring up that chromosome in multiple organisms so we will add another organism constraint. Click on the Organism to reveal its attributes then click on constrain next to Genus. In the resulting pop-up window, slect “=” (equals) then “Equus” for the chromosome 18 of horse.
Example 2, Step 2 Adding constraints to the Chromosome ID and Organism
Click on Show results and the query will result in all protein-coding genes on the Chromosome with constrained ID and organism. Note that the number of results has been reduced with the addition of the constraint.
Example 2, Step 3 Result table after constraining by Chromosome ID and Organism
Example 3: Querying for Protein Coding genes on a particular chromosome and their exons¶
This last example builds upon the previous queries to display all exons for each gene on a particular chromosome. Again, note the “Trail: Query” text at the upper left of the results table. Clicking on the “Query” link will bring you back to the query that generated the table to allow for edits without having to build a new query. Scroll down to Exon feature class and select the “+” (plus sign) next to Exons to display its attributes. Click Show next to Length and Exon Identifier.
Example 3, Step 1 Expand exon attributes and add fields to the query
The Query Overview shows the query in progress with the selected fields. Also notice that a third type of icon, a blue square, appears next to some attributes. Clicking on a blue square icon brings up a window where the query Join Style may be modified. When adding a constraint, you can decide whether you want to show only those results with the information (genes with exons) or all results and the constrained feature if it exists (e.g., all genes and indicate exons if they exist). Click on the blue square icon next to Exon collection to bring up the Switch Join Style window. The default option is to show only Genes if they have a exon (inner join). Change this to Show all Genes and show Exons if they are present (outer join) then click Add to query.
Example 3, Step 2 Select join style for exons
Then click “Show results” to run the new query.
Example 3, Step 3 Query results with exon constraint
The results table now lists a new column Gene Exons, which we added to the query. If we look at the second row in the table, it lists 12 exons. Click on the 12 exons link to expand that entry. That column now has additional rows containing the Exon identifier and Length for each of the 12 exons.
Example 3, Step 4 Query results with exon column expanded
In changing the join style to an outer join, the exons have been grouped together by gene making it easier to determine how many exons are contained in each gene. If the same query is run with the default join (outer join) of Show only Genes if they have an Exon, the results table adds a new row for each new exon rather than grouping exons by gene.
Example 3, Step 5 Query results with default join style run for genes containing exons
Report Pages¶
All objects in FAANGMine (e.g., gene, protein, transcript, publication) have report pages that can viewed after running a query. It allows users to view all available information for that object while providing links to related objects. As an example, we can revisit the templates example. In the list of templates under the Templates tab on the FAANGMine home page, select Gene -> Homologues to query FAANGMine to retrieve all homologues for a given gene. Enter “GSTM1” into the the LOOKUP search box then click Show Results. In the results table, note that every entry is contains a link. You can mouse over any link to bring up a summary of that object. If we hover over the first Gene ID, we can see a summary box that includes
Summary for gene entry in query results table
Clicking on that same item will bring up its report page that includes a comprehensive for gene GSTM1. The report page header shows the Gene ID and its Biotype, for this example, protein coding. The tabs at the top of the page in the Quick Links menu bar quickly bring you to the data listed. The column on the right side of the report page displays external links to other Mines and databases.
Report page for protein-coding gene
The content of the report page is divided into categories based on the type of information provided for that particular object. Clicking on links within each category bring up more details about the objects of interest.
Summary¶
The Summary section near the top of the report provides information on the gene such as its length, chromosome location, and strand information. Users can also get the complete FASTA sequence of the gene by clicking on the FASTA tab.
Transcripts¶
The Transcripts section contains information about the gene model, such as transcripts and exons. Links to FASTA files are included where applicable.
Proteins¶
The Proteins section provides information about the protein product of the gene. The comments section gives a brief description about the protein along with the UniProt accession and links to any outside data sets.
Function¶
The Function section displays Gene Ontology annotations for a gene. Annotations are divided into three categories:
- Cellular Component
- Molecular Function
- Biological Process
The GO terms are displayed along with the evidence code indicating how the annotations were derived. A results with Pathway information is also displayed if applicable.
Homology¶
The Homology section provides information for all homologues. The first portion displays a summarized view of the homologues reported in different organisms. The next portion provides more detailed information about the homologue, the type of homologue and from which dataset the information was obtained all displayed in a results table.
Interactions¶
The Interactions section provides interaction information. For GSTM1 there are no interaction information available but for genes that do have interaction information, a network is displayed showing all interactors for the current gene.
Publications¶
The Publications section displays a table of publications related to the gene with links to full citations.
Other¶
This last section provides miscellaneous information that do not fit into any of the above categories. This example lists protein coding annotations and their sources.
Genomic Regions Search¶
The Genomic Regions Search is a tool to fetch features that are within a given set of genomic coordinates or are within a given number of bases flanking the coordinates.
To begin this type of search, click the Regions tab on the menu bar. A form will appear asking for the search parameters (organism, feature types, genomic coordinates, etc.)
Genomic Regions search form
The coordinates must have one of three formats:
- chromosome_number:start..end
- chromosome_number:start-end
- chromosome_number start end (tab delimited)
Click on the input examples above the text input box (number 4) to view a representative set of coordinates in each format. Click the Genome coordinates help link near the top of the form for more detailed information on the input format requirements.
During a search, regions may be extended on either side of the genomic coordinates using the slider or by entering text in the field to the left of the slide bar. There is also the option to perform a strand-specific region search using the checkbox at the bottom of the form (number 6)
As an example, select B. taurus from the Select Organism drop-down, and ARS-UCD1.2 as the Assembly. Slick the box next to Select Feature Types to uncheck all of the boxes, then check the box next to Gene, and enter the following coordinates into the genomic regions search text field:
14:2000000..2800000
Click the search box to conduct the genomic regions search. If there are no overlaps within your search coordinates, the search can be done again with the search region extended using the slide bar or entering text into the search box (e.g., 10k).
Genomic Regions search example with Bos taurus
The search results page presents a list of features present within the genomic interval that was searched. In this case, the feature type was limited to Gene. The results may be exported as tab-separated or comma-separated values. If they contain genomic features, there is also the option to saved the results in GFF3 or BED format. The FASTA sequences of the features may also be downloaded. Links within the features provide detailed reports. If users are interested in creating a list of particular features from the result page then they can filter based on feature type (if applicable), shown in red box, and click on Go.
Genomic Regions search results
Lists¶
Creating Lists¶
Users may create and save lists of features, such as gene IDs, transcript IDs, gene symbols, etc. The list tool searches the database for the list items and attempts to convert each identifier to the selected type. Click on the Lists tab from the menu to access the full list upload form. A short version of the form is also in the Quick List box on the home page.
List upload form
Quick list from FAANGMine home page
As an example, enter the following comma-separated identifiers into the Lists upload form under the Lists tab. Notice that they do not have to be in the same format. A Summary table is displayed with the results of searching for each of the five identifiers in the list.
CAPN2, ENSCHIG00000014802, BTG1, XDH, 101107826
Leave the Select Type drop-down menu to Gene and the Organism drop-down to Any. Click on Create List. Note that you can also upload a list from a .txt file.
List Example: Search results for list of identifiers
The summary table provides information regarding those identifiers that had a direct hit without any duplicates. If there are any duplicates, users can decide to add the relevant entries individually by clicking on the Add button under the Action column or choosing the Add all tab. Here we will click Add all. Once the selections have been added, the list can be saved by clicking the Save a list of 66 Genes button on the top of the summary table. Name the list by entering text into the Choose a name for the list box at the top of the results page.
List Example: Saving list of identifiers
After the list is saved, users are presented with a List Analysis page. This page provides users with widgets to perform analyses on gene lists that they have created.
List Example: Analysis for gene list
The selection of widgets provided on the List Analysis page depend on the contents of the list. The available widgets for this list example include:
- Gene Ontology Enrichment
- Publication Enrichment
- Pathway Enrichment
- Orthologues
List Example: Displayed widgets for list analysis
Saving Lists¶
To see your saved lists, click the View tab on the Lists page. If not logged in, lists will be saved temporarily during your current session. However, you must be logged in to save your lists permanently. Further analyses of lists can be done with the Actions links at the top of the list. The links become active once lists are selected for analyses. Saved lists may also be accessed from the MyMine menu tab.
List Example: Saved user lists
MyMine¶
MyMine serves as a portal where logged-in users may manage their lists, queries, templates, and account details.
To access MyMine, click on the MyMine menu tab. A submenu appears with six options:
Lists - Lists saved by the user when logged in.
History - List of most recently run queries.
Queries - List of saved queries.
Templates - Templates created or marked as “favorite” by the user.
Password - Password reset form.
Account Details - User preferences form.
Saved lists found under MyMine. Note that currently saved lists can be selected for analyses to contribute to new lists.
API¶
An API is available for users who would like to programmatically access FAANGMine.
Perl, Python, Ruby, and Java are the languages supported by the InterMine API.
For more detailed information, view the InterMine documentation.
Data Sources¶
The Data Sources table provides a description of the datasets that are integrated into FAANGMine, along with their download location, version or release, citations wherever applicable, and any additional comments.
BovineMine Data Sources table
How to cite¶
FAANGMine is a project supported by the National Science Foundation to address the need for a high performance data mining resource that enables fine-grained querying and integrating the heterogeneous FAANG data with existing information, such as functions of known genes and research datasets.
For more generic examples on how to use InterMine, click here. These are tutorials created by FlyMine that showcase the different features of InterMine.