Gemina Home Page Tutorial

Gemina Home Page

Additional Resources

• Contact Us: Click on the Contact Us link to send us questions, comments or bug reports.
• Download Gemina: Download Gemina's up-to-date Ontologies and Controlled Vocabularies as well as the code used to develop both the database and webpage. As part of the Gemina project we have developed three controlled vocabularies for Geographic Location, Transmission Method and Reservoirs. We have also developed three ontologies for Disease, Anatomy and Symptoms.

Quick Start

• From the Selection Summary box select a metadata category to explore or query the Gemina database.
• This selection will open the corresponding Tree View where you can query the data by text queries or browse the hierarchical tree.
• Scroll down to view the expanded Tree View

Gemina Home Page Tutorial

• Select any of the available metadata types. The corresponding Tree View will appear to right.
• Select Pathogen to explore bacterial or viral infectious pathogens. Currently the Gemina database contains curated metadata for NIAID category A-C bacteria from the Actinobacteria, Chlamydiae, Firmicutes, Proteobacteria phyla and all influenza subtypes and strains.
• Gemina has been designed to include all viral and bacterial pathogens. Additional data are being added to Gemina in an on-going basis.
• Select Toxins to explore infectious toxin pathogens.
• Select Host to explore the variety of animal hosts.
• Select Reservoir to query Gemina and retrieve a pathogen's related metadata based on it's curated animal, environmental or human reservoir.
• Select Environmental Sources to explore non-living sources of pathogens.
• Select Disease to explore the human and animal infectious diseases associated with bacterial and viral pathogens.
• The disease Tree View is organized primarily by body system. Additionally, the Infectious and parasitic diseases node encompases Bacterial diseases, Diseases due to Viruses, Rickettsioses and Zoonotics.
• Select Anatomy to query the human or animal hosts's portal of entry. The anatomy ontology includes cell types, tissues, sense organs, animal structures and body systems.
• Select Transmission Method to view the direct or indirect methods by which the pathogen enters the host organism.
• Select Symptoms to explore symptoms associated with bacterial and viral pathogens.
• Select Location to explore locations associated with bacterial and viral pathogen incidents.
• Scroll down this page to see the Disease Tree View and explore additional options for querying Gemina.

Gemina Query Page Tutorial

Tree View Options

• Here is an expanded Disease Tree View.


• Data in the Tree View can be queried from the Search box. Type in a search string and click on Search Tree .
• In the tree view, click on the green plus sign [+] to add terms to the Selection Summary box.
• Terms followed by a green plus sign are selectable and reflect data present in the Gemina database.
• Click on the terms to view children terms and browse the tree.


• Text Queries:Terms may also be added to the Selection Summary box by submitting a text query at the top of the tree view. Query results are summarized at the top of the Tree View. Clicking on "results associated with data" will populate the Selection Summary box with all of the results. Individual results, highlighted in blue, can be added one at a time to the 'Selection Summary' box by clicking on them or the adjacent green plus sign [+].
• Removing Terms: Terms can be removed from the Selection Summary box by clicking on adjacent red X. All terms can be removed from the Selection Summary box by clicking on the "Clear All Selections" button at the bottom of the Selection Summary box.
• Submit your list of query terms against the Gemina database by clicking on either "View Infections" or "View Incidents" at the bottom of the Selection Summary box to view infection systems or incident systems respectively.

Gemina Query Page Tutorial

• In this example, multiple metadata types were queried to form a complex-multiterm query. The results of those queryies are shown in the Selection Summary box. Once all of the terms you wish to include in your Gemina query are in the Selection Summary box, click on Submit to query the Gemina database.
• For this example, the Host data were queried for rat, returning three hits, one of the vector-borne transmission methods was selected from the Transmission Method Tree View and the Disease data was queried for entries matching "Plague". The results for the Disease search are shown in this image.
• Submit your list of query terms against the Gemina database by clicking on either "View Infections" or "View Incidents" to view infection systems or incident systems respectively. The "Clear All Selecitons" button wipes the query currently being built.
  • View Infections: Retrieve a pathogens unique set of hosts, diseases, methods of transmission and anatomical portal of entry.
  • View Incidents: Retrieve a pathogens unique outbreak metadata including location, date, host age and host gender.

Gemina Infection Results Page Tutorial

Gemina Infection Report

• The Gemina Infection Report presents the user with a tabular display of metadata organized by pathogen. This example uses the search term 'Bacillus anthracis' to return infection metadata describing the what, how and who of an infection system.


• The toolbar found on the Gemina Infection Report allows for the execution of several options on the metadata returned from a query:
• View Query: Displays the current query.
• Edit Query: Returns to the homepage with the current query presevered allowing for removal or addition of terms.
• Tools: Operations which can be exuted on the results data.
  • Insignia: Allows for the submission of either all results or a user-selection of results to the Insignia pipeline.
• Download Options: Available formats to download the results data.
  • TXT: Downloads the results to plain text file.

Total Results

• Total results are displayed here alongside a link to view related search results.
• The related search results link will attempt to find results that are similar to the ones retrieved from the current query.

Main Results Table

• The main results table displays the data returned from the Gemina database based off the query submitted.


• Results data is sectioned off into pathogen blocks. The header of each block contains the name and a link to the NCBI taxonomy page for the given pathogen. If reservoirs exist for the pathogen they may also be displayed. Each header also contains a checkbox that can be used to specify specific pathogens for further operations.
• The rows of data displayed are described below:
  • Ref: Reference from which this row of data was curated. Each reference contains a link to the source.
  • ID: This is a Gemina specific ID used to identify infections and incidents.
  • Source: The source of this infection system. includes any organism, object, or medium on or in which a pathogen may survive or be transported. Links to the source NCBI taxonomy page are made available when they exist.
  • Transmission Method: Describes the means by which the pathogen is transfered into the host..
  • Host/Reservoir: The host/reservoir for this infection system. Links to the host/reservoir NCBI taxonomy page are made available when they exist.
  • Disease: Includes all infectious diseases caused by the pathogen.
  • Anatomy: The portal of entry for this infection system. Includes the body systems, tissues, cell types and animal structures which are the portals of entry for the pathogen.
  • Symptoms: Any symptoms that may exist for this infection system
  • Incidents: Incidents of this infection system if any exist.

References

• References are the sources from which a row of results is curated. Two different sources exist in Gemina:
  • NCBI reference: An NCBI reference is a source that comes from NCBI. More times than not this will be Pubmed .
  • External reference: Any non-NCBI reference.

Incidents

• The Incidents column contains links to any incidents that are associated with this infection system.
• The number in the colum indicates how many incidents are associated with this infection system.
• Clicking on the number in the column takes the user to the incidents result page.

Gemina Incident Results Page Tutorial

Gemina Incident Report

• The Gemina Incident Report presents the user with a tabular display of metadata organized by pathogen. This example uses the search term 'Bacillus anthracis' to return incident metadata describing the where, when, and how of infection system cases.


• The toolbar found on the Gemina Incident Report allows for the execution of several options on the metadata returned from a query:
  • View Query: Displays the current query.
  • Edit Query: Returns to the homepage with the current query presevered allowing for removal or addition of terms.
  • Tools: Operations which can be exuted on the results data.
    • Insignia: Allows for the submission of either all results or a user-selection of results to the Insignia pipeline.
    • GoogleMaps: Plots a single incident or multiple incidents to an extenal full-screen GoogleMap
  • Download Options: Available formats to download the results data..
    • TXT: Downloads the results to plain text file.
    • GoogleEarth: Generates a GoogleEarth ready KML file. This file plots incidents on a virtual map that is viewable in GoogleEarth.

Total Results

• Total results are displayed here alongside a link to view related search results.
• The related search results link will attempt to find results that are similar to the ones retrieved from the current query.

Main Table

• The Incident Report's main result table contains all the metadata returned from the database in tabular format. Eight columns organize the metadata in the table:
  • Ref: Reference from which this row of data was curated. Each reference contains a link to the source.
  • ID: This is a Gemina specific ID used to identify infections and incidents.
  • Location: The location at which this incident occured.
  • Disease: The infectious diseases contracted in this incident.
  • Host: The host for this specific incident. Links to the host/reservoir NCBI taxonomy page are made available when they exist.
  • Date: The data at which this incident occured.
  • Gender: Gender of the host.
  • Age: Age of host.
  • Transmission ID: An internal identifier keeping track of each step in an outbreak. This ID links back to the infection system causing the incident.

References

• References are the sources from which a row of results is curated. Two different sources exist in Gemina:
  • NCBI reference: An NCBI reference is a source that comes from NCBI. More times than not this will be Pubmed .
  • External reference: Any non-NCBI reference.

GoogleMaps

• The globe icon found next to each Location name opens a separate window plotting the incident in GoogleMaps.
• A small amount of metadata is included in the plotted map:
  • Pathogen Name
  • Location Name
  • Date
  • Links:
    • : Links to the NCBI taxonomy page for the pathogen.
    • : Links out to Genbank for any sequence data that may exists for the pathogen.
    • : Links back to the infection system for this incident.