BGS Hosted Metadata
Molluscan Shell Matrix Proteins
The database contains fasta sequences from UniProt and associated metadata for molluscan shell matrix proteins (SMPs). The database only contains SMPs that have been experimentally validated to be present in molluscan shell matrices (based on the publication(s) attached to the UniProtID). Metadata includes information on functional domains present in the sequence, as detected by InterproScan.
With the advent of Next Generation Sequencing technologies, it is computationally resource intensive to run sequence similarity algorithms on all published data. Moreover, it is impractical to sort through hundreds of sequence similarity search results when working with non-model organisms, since pre-established functional annotations of sequences are generally not available. Therefore, this database was created in order to provide a targeted molluscan biomineralization dataset for sequence similarity algorithms (such as BLAST).
Database created as part of doctoral research, funded under Marie Curie Innovative Training Networks (ITN) - Calcium in the Changing Environment (CACHE - Grant agreement 605051).
Simple
- Date (Creation)
- 2019-01-24
- Date (Revision)
- 2019-01-24
- Date (Publication)
- 2019-01-24
- Date (released)
- 2019-01-24
- Edition
-
1.0
- Unique resource identifier
- https://doi.org/10.5285/c42314b9-089e-48e7-b08e-8f664f5dc71c
- Codespace
-
doi
- Unique resource identifier
- GB/NERC/BAS/PDC/01132
- Codespace
- Other citation details
-
Please cite this item as: Yarra, T. (2019). Molluscan Shell Matrix Proteins (Version 1.0) [Data set]. UK Polar Data Centre, British Antarctic Survey, Natural Environment Research Council, UK Research & Innovation. https://doi.org/10.5285/c42314b9-089e-48e7-b08e-8f664f5dc71c
- Credit
-
No credit.
- Status
- Completed
- Point of contact
-
Organisation name Individual name Electronic mail address Role British Antarctic Survey, Natural Environment Research Council, UK Research & Innovation Yarra, Tejaswi Author NERC EDS UK Polar Data Centre Point of contact
- Maintenance and update frequency
- As needed
- Maintenance note
- Completed
- Theme
-
-
Biomineralization
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Molluscs
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SMPs
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Shell Matrix Proteins
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Shell formation
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GEMET - INSPIRE themes, version 1.0
- Access constraints
- Other restrictions
- Other constraints
- no limitations to public access
- Access constraints
- Other restrictions
- Other constraints
- no limitations
- Use constraints
- License
- Other constraints
- Open Government Licence v3.0
- Use constraints
- Other restrictions
- Other constraints
-
Data released under Open Government Licence V3.0:
- Unique resource identifier
- url
- Codespace
-
url
- Association Type
- Cross reference
- Spatial representation type
- Text, table
- Language
- English
- Character set
- UTF8
- Topic category
-
- Biota
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- Supplemental Information
-
It is recommended that careful attention be paid to the contents of any data, and that the author be contacted with any questions regarding appropriate use. If you find any errors or omissions, please report them to polardatacentre@bas.ac.uk.
- Title
-
European Petroleum Survey Group (EPSG) Geodetic Parameter Registry
- Date (Publication)
- 2008-11-12
- Cited responsible party
-
Organisation name Individual name Electronic mail address Role European Petroleum Survey Group
Publisher
- Unique resource identifier
- urn:ogc:def:crs:EPSG::3031
- Version
-
6.18.3
Distributor
- Distributor contact
-
Organisation name Individual name Electronic mail address Role NERC EDS UK Polar Data Centre Distributor
- Distributor format
-
Name Version application/vnd.ms-excel text/x-fasta text/plain
- Units of distribution
-
bytes
- Transfer size
- 445440
- OnLine resource
-
Protocol Linkage Name WWW:LINK-1.0-http--link
https://ramadda.data.bas.ac.uk/repository/entry/show?entryid=c42314b9-089e-48e7-b08e-8f664f5dc71c Get Data
- Units of distribution
-
bytes
- Transfer size
- 445440
- OnLine resource
-
Protocol Linkage Name WWW:LINK-1.0-http--link
https://ramadda.data.bas.ac.uk/repository/entry/show?entryid=c42314b9-089e-48e7-b08e-8f664f5dc71c Get Data
- Units of distribution
-
bytes
- Transfer size
- 445440
- OnLine resource
-
Protocol Linkage Name WWW:LINK-1.0-http--link
https://ramadda.data.bas.ac.uk/repository/entry/show?entryid=c42314b9-089e-48e7-b08e-8f664f5dc71c Get Data
- Hierarchy level
- Dataset
- Statement
-
Methodology:
Data was gathered by mining metadata from Trembl database for various biomineralization specific keywords. Example keywords include: Molluscs, shell, bivalve, aragonite, calcite, prismatic, foliated, mantle, mantle edge, central mantle, pallial mantle, etc. Only SMPs uploaded to Uniprot were included in this database. The database only contains SMPs that have been experimentally validated to be present in molluscan shell matrices (based on the publication(s) attached to the UniProtID). Uniprot entries for only mantle specific sequences were not included, since all such sequences were determined to be biomineralization related based on sequence similarity results to the proteins identified in shell matrices, and were not experimentally validated.
Data collection:
Data was collected from Uniprot ( https://www.uniprot.org/).
Data quality:
Database is based on uploaded Unioprot IDs entries until JULY 2018. No major publications have since been released that match the criteria to be included in the database. Missing values are only present in the domain columns - A missing value indicates that there were no functional domains detected in the sequence, based on InterproScan results from Interpro databases.
Metadata
- File identifier
- c42314b9-089e-48e7-b08e-8f664f5dc71c XML
- Metadata language
- English
- Character set
- UTF8
- Hierarchy level
- Dataset
- Hierarchy level name
-
dataset
- Date stamp
- 2019-01-24
- Metadata standard name
-
ISO 19115 Geographic Information - Metadata
- Metadata standard version
-
ISO 19115:2003(E)
- Metadata author
-
Organisation name Individual name Electronic mail address Role NERC EDS UK Polar Data Centre Point of contact
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