Difference between revisions of "MPDL Demonstrator Marine Microbiology"

Revision as of 11:05, 25 January 2011

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Participants[edit]

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

Short description[edit]

Use cases[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

See Annotator service

Important things[edit]

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 eg. 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, see also http://www.arb-silva.de/projects/contextual-data/
- contextual data, see also http://gensc.org/gc_wiki/index.php/MIENS
Blogs from the expeditions and probes see http://wissenschafts-blog.abendblatt.de

@@ Line 19: / Line 19: @@
 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 [http://www.arb-silva.de/ 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 image below (note that mock-up and implementation may differ after the revision with the Institute):
+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 new Silva Annotation===
+===Create Silva Annotation===
 [[Image:SilvaAndPubMan.png|1200px]]
-*User chooses to create a Silva Annotation for a particular Publication
+* 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)
+* 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 a URL of the Silva resource
+* User enters an URL of the Silva resource
-*The System fetches the Silva resource data from predefined web service (e.g. Silva service) and populates the annotation fields (e.g. description, location, etc.) correspondingly
+* 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
-*User adds additional metadata if necessary (e.g. comment) and saves the Annotation
+* The user adds additional metadata if necessary (e.g. comment) and saves the annotation
 ===View Annotation===
 [[Image:Annotation-Browser-Publications-Case.png|1200px]]
-*User chooses to view Annotations for the 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 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 respective service icon (e.g. GeoBlast, EMBL)
-===List my publications linked to the annotated resources for inclusion in my web pages===
+* 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? --[[User:Kristina|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.
-*User chooses to export his publications into a new "APA-annotated" citation style
+* The user chooses to export his publications into a new "APA-annotated" citation style
-*User defines the search criteria to get a list of publications
+* 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:
+* The system provides an APA-annotated citation style (with additional information on annotated resources), as in the example below:
+[[Image:SilvaCitation.png|border|1000px]]
-  [[Image:SilvaCitation.png|border|1000px]]
+=== Search based on Coordinates ===
-===Provide coordinates of a search area and retrieve a list of all publications and Silva resources related to the institute expeditions===
+Aim: To provide coordinates of a specific area of interest and retrieve a list of all publications and Silva resources related to this area.
 [[Image:BlastWithPublications.png|1200px]]
-*User enters coordinates of a search area into the search interface(see Note below)
+* 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 Silva sequences for the requested coordinates
-*The system retrieves a list of publications for the requested Silva sequences
+* 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 related publications into a new "APA-annotated" citation style
+* 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
+Note: This use case may be used as an integration with the GeoBlast web service
 ===Related services and information===