MPDL Demonstrator Marine Microbiology

This is a protected page.

Participants

• MPDL
• Max-Planck-Institut für marine Mikrobiologie in Bremen see MPIMB

Short description

• General about the institute
• Departments and groups

Use cases

• I would like to have a list of my publications linked to the Silva resources I have been working on represented on the home page of my research group and on my personal home page
  • or in other wording: as a user of PubMan i would like to link my publication to one or more Silva resources via Silva accession ID, and have the Silva accession ID included into the PubMan citation
• I would like to be able to provide search by Silva accession ID and retrieve all publications related to this ID
• I would like to provide coordinates of a search area, and be able to retrieve a list of all publications and Silva resources related to Marine Microbiology expeditions in that area.
• I would like to have a list of all publications related to an expedition
• In my blog http://wissenschafts-blog.abendblatt.de I would like to provide an RSS feed of the publications that reference the expedition the blog is about

Demonstrator

In the basic demonstration scenario, PubMan will be extended with a functionality to annotate a publication by linking it to external data resources of interest e.g. probes, genomes, meta-genomes etc. In the first stage the Silva database will be considered as a repository where such data resources reside. A screen Mock-up for the envisioned scenario is displayed in the images below (note that mock-up and implementation may differ after the revision with the Institute).

Create Silva Annotation

• The user chooses to create a Silva Annotation for a selected publication
• The system offers a form for entering an annotation (the form also contains a list of icons for available services for a Silva annotation e.g. GeoBlast, Map Server, EMBL-EBI)
• User enters an URL of the Silva resource
• The System fetches the Silva resource data from a predefined web service (e.g. Silva service) and populates the annotation fields (e.g. description, location, etc.) correspondingly
• The user adds additional metadata if necessary (e.g. comment) and saves the annotation

View Annotation

• The user chooses to view all annotations for a selected publication
• The system displays the Annotation Browser and lists all annotations for the selected publication
• The user may also browse through other types of Annotations that exist for the selected publication
• The user may decide to modify an annotation or add another annotation of a particular annotation type
• The user may decide to invoke an external service for the target source (i.e. Silva resource) referenced in the annotation, by triggering a respective service icon (e.g. GeoBlast, EMBL)
  • What will happen when such a service is triggered here? --Kristina 11:05, 25 January 2011 (UTC)

Export Annotation

Aim: To create a list of my publications which includes the annotated resources as links. This list than can be included on my web page.

• The user chooses to export his publications into a new "APA-annotated" citation style
• The user defines the search criteria to get a list of publications
• The system provides an APA-annotated citation style (with additional information on annotated resources), as in the example below:

Search based on Coordinates

Aim: To provide coordinates of a specific area of interest and retrieve a list of all publications and Silva resources related to this area.

• The user enters the coordinates of a search area into the search interface
• The system retrieves a list of Silva sequences for the requested coordinates
• The system retrieves a list of publications for the requested Silva sequences
• The system displays a map showing the hits for sequences and a list of all related publications per hit into a new "APA-annotated" citation style

Note: This use case may be used as an integration with the GeoBlast web service

Related services and information

• See Annotator service

Important things

• Chemistry - analysis, analytical chemistry, nucleic acid analyses, genome analysis and metagenomics, field work, mathematical simulations, experimental visualizations
• Publications
• Expeditions
• Projects (experimental - field research and probes)
• Locations
• Facilities and methods
• RNA sequences for all three domains of life (Bacteria, Archaea and Eukarya)
• FISH and probes - online resource for information on the identification of individual microbial cells by fluorescence in situ hybridization (FISH) with ribosomal RNA-targeted oligonucleotide probes
• Protocols of the SILVA ribosomal database project (e.g. http://www.arb-silva.de/fileadmin/graphics_fish/SILVA_FISH_protocols_fixation_100618.pdf)
• Marine ecological genomics, integrating genomic, metagenomic and ribosomal RNA data with primary environmental data and curated metadata
• SILVA - on-line resource for quality checked and aligned ribosomal RNA sequence data, free for academic use
  • contextual data (data about data), see also http://www.arb-silva.de/projects/contextual-data/
  • contextual data, see also http://gensc.org/gc_wiki/index.php/MIENS
    • What is the difference between these two contextual data? --Kristina 11:14, 25 January 2011 (UTC)
• Blogs from the expeditions and probes see http://wissenschafts-blog.abendblatt.de

--> Actually I do not understand the purpose of this list (important things) here. Some things are only terms, others are linked to some data. I think it would be usefull to explain the things listed here more detailed, because at the moment, I do not understand this part. --Kristina 11:14, 25 January 2011 (UTC)

Max Planck Digital Library

Publication Management

Identifier

Really Simple Syndication

European Molecular Biology Laboratory

Uniform Resource Locator

Coordinated Universal Time

American Psychological Association