Our Online Database
The AMCC online searchable database, built and maintained by M. Breedlove, and populated by A. Corthals, uses the open source products Apache, MySQL , PHP.
Apache, PHP and MySQL are open source technologies that allow one to create powerful and fast database-generated Web site applications. Apache is the most popular Web server, PHP is an open-source server-side scripting language and MySQL is a fast, reliable, open-source database management system.
The data available on the AMCC website constitute a subset of data from our relational database Freezerworks, loaded into the MySQL database. This allows the AMCC to have better control of the amount of data published on the web.
Database Codes
...will be available soon for you to download.
In the meantime, this is what the schema of the relational database looks like. This file is provided and owned by Mark Breedlove:
Database Features
This mySQL based database hosts the taxonomic data of the AMCC's relational database (Freezerworks Unlimited), as well as any bibliographical references and the e-vouchers of a given specimen. Additionally, the database is linked out to the NCBI taxonomy website and GenBank allowing for an easy access to any DNA sequences and any changes in its taxonomy.
SEARCH
The database allows the user to search by taxonomical nomenclature only, or to combine the search with locality data, using 3 scroll down menus (Continent, Country, Body of Water) and/or Specific locale
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Scroll down menus (Continent and Country) close-up
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The upper right table allows the user to browse by Phylum, all the way down to a specific specimen.
It is also possible to search, in a scroll down menu, by Department/Partner
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Drop down Dept/Partner menu
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It is also possible to search by AMCC #, Genbank sequence accession #, or NCBI taxonomy #
SPECIMEN RECORD
The specimen record offers several features (from the top down)
AMCC #: necessary for user to request a specimen
Taxonomy: Phylum, Class, Order, Family, Subfamily, Genus and Species (on top, with Authority)
Locality: Continent, Country, higher geo-polotical division 1 and 2, specific locality
The taxonomic history records any noteworthy historical changes to a specimen’s taxonomic classification.
Dept/Partner indicates which of the AMNH departments has the responsibilty for the tissue specimen (i.e. gives out approval for loans) as well as where the voucher (if present, indicated by the presence of Voucher #) is held
Sample ID is a field which allows user to search by an other ID number than the AMCC. It has been deemed useful in the Wolbachia project case, if users want to refer to their own sample by another mean than browsing the specimens by Dept/Partner
LOAN REQUEST LINKS
A simple link takes you to the AMCC website page explaining the loan procedures. This link is present in the banner on top of each pages of the database as well as on each specimen record.
GENBANK/NCBI LINKOUT
The database is designed to integrate with the National Center for Biotechnology Information's Entrez indexing and retrieval engine and its LinkOut service (http://www.ncbi.nlm.nih.gov/entrez/linkout/). This allows AMCC records with nucleotide sequence accession numbers to link out to corresponding pages on the NCBI Genbank and Taxonomy databases and inversely for GenBank sequences to link out back to the AMCC.
EVOUCHERS
The term "E-Voucher" has been defined by Monk and Baker (2001) as follows: "An e-voucher is a digital representation of a specimen. An e-voucher may be ancillary to a classical voucher specimen or it may be the only representative of the specimen in the collection." Traditionally, voucher specimens deposited into museum collections were morphological vouchers, and in most cases, consisted in the cadaver of the whole animal. In the case of a frozen tissue repository, this traditional definition of a voucher becomes not only impractical, but for the majority of animal sampled, simply impossible to apply. Thus, the digital picture of the specimen sampled becomes the morphological voucher in the many cases where the remains of the animal sampled are unobtainable (though it does not, by any mean, replace the value of a true physical voucher). To that effect, the AMCC has linked, whenever possible, the specimen records to digital images (hosted by the museum's Digital Library server), making for a complete connection between sequence data and the visual identity of the specimen examined.
Our Database Software: FreezerworksTM
The customization of FreezerworksTM 5 into FreezerworksTM Unlimited was made to fit the database demands of a facility such as the AMCC. After months of collaboration between Dataworks Development, Inc. and the AMCC, the product was finally launched in April 2002.
The main and most important customization brought to Freezerworks was the possibility to add and customize as many field as the facility would require. In the case of a collection as disparate as the AMCC's, such customisation are daily routine as the staff must adapt the database to the requirement of each batch of specimen being accessioned.
Here is an example an AMCC specimen record:
Freezerworks in its AMCC customized version contains over 80 fields and 8 tabs for each and every specimen.
The use of Freezerworks at the AMCC
The structure of Freezerworks at the AMCC follows the requirements of data entry for the type of specimen accessioned. To that effect, the sample entry sheet view is divided in 8 tabs: 5 customized tabs, and three mandatory tabs.
The customized tabs are:
- Administrative Data: records all administrative data pertaining to a specimen. This includes all associated sample ID, Registrar ID #, Department partner #, ISIS #, evoucher#, ect. The name of the donor and expedition or field collection trip during which the specimen was acquired is also recorded here, as well as the level of access to the given specimen.
- Taxonomy: records all taxonomic information pertaining to a specimen. This includes taxonomic history notes which records the changes in the specimen taxonomy, or any other taxonomical information which does not fit in the traditional taxonomical fields. It also records several levels of bibliographical references associated with the given specimen, from Authority, to Reprints.
- Field Data: records all data captured on the field trip during the specimen's collection. This includes several levels of geographical localisation, as well as the specimen field preparation method, the habitat description and who prepared it.
- Aliquot: records the exact position,as well as the type, of each aliquot (vial) of a given specimen in the AMCC freezer. Example: specimen 10024 has got 5 aliquots vial 1:heart, Freezer1, Rack 2, Position 32; 2:muscle, Freezer1, Rack 2, Position 33; 3:liver, Freezer1, Rack 2, Position 34; 4:Small intestine, Freezer1, Rack 2, Position 35; 5:intestine, Freezer1, Rack 2, Position 36. This tab also record the initial and current weight, as well as the preservation history of each aliquot and protocols they have been through.
- Physical characteristic: records all physical characteristic associated to a specimen, from different types of measurements of the animal to its mold status, reproductive status as well as birth type.
The mandatory tabs:
- Notes: records additional notes pertaining to the specimen, but not belonging to any of the previously described tabs
- Transaction: records each physical event for each aliquot of a given specimen, such as loan, DNA extraction etc.
- Audit Trail: records each data entry and modification within one given record. It includes the name of the person who entered it, and the date and time, allowing easy QCs.
Why Freezerworks was chosen by the AMCC:
- Capable to run on both PC and Macintosh platforms
- Tailor the program to match all freezer/refrigerator rack and label systems
- Create as many user-defined fields as needed
- "Point and click", "drag and drop" through freezer data
- Find samples quickly with a powerful search engine
- Search and move through freezers using "Explorer" style tree structure
- Take advantage of the flexible report writer and content rich pre-configured reports
- Print bar code and human readable vial labels designed to withstand long-term cryogenic storage and thawing processes
- Configure bar code and human-readable labels
- Meet all regulatory requirements with an automated audit trail
- Import data from existing databases and spreadsheets
- Configure to meet your own user, freezer, and data security needs
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About Freezerworks
Specimens accessioned in the AMCC are indexed using a relational database application program called FreezerworksTM.
Each specimen is given a unique barcode ID which is then printed as
both barcode and human readable number on cryo-labels.
Program Conventions
(FreezerworksTM Unlimited User's Guide,
Dataworks Development, Inc. p. 8-10)
Keys to understanding and using FreezerworksTM Unlimited
In this section we discuss the language of database management. As is
true with many professions, database management people have their own
language - a set of terms that they use to describe the things that
relational databases do. In this section, you we define terms useful for
understanding relational databases in general, and Freezerworks in
particular.
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The Relational Database
Model
The Relational Database Model is a theory for designing databases that
was first developed by an IBM database theoretician named E.F. Codd. Codd
developed his model by applying mathematical Set Theory to the problem of
database design. In this section, we will discuss the practical
application of the Relational Database Model, as it applies to the
Freezerworks database.
Simply stated, the Relational Database Model is a collection of tables
(also known as "flat files") with the following characteristics:
Specialization: Each table "specializes" in storing a certain type of
information. This information is stored in fields. When an item that
contains field information is completed and stored in the table, this
item becomes a record in that table.
Key Fields: Each table holds a key field. The data in this key field
is unique - that is, no two records will have exactly the same data in
this key field. (For example, there will only be one Sample with the
Internal ID number 101). This unique quality is what makes it possible to
distinguish one record in the table from all other records in the
table.
Indexed: Each key field is indexed for fast searches. Other fields may
be indexed as well.
Relations: So that they can share information, many of the tables are
related to each other. Hence the term, "Relational Database Model."
Duplicated Related Fields: To manage the relationships, we copy the
Key Field data into the related records. For example, when we save a
Sample, we copy the Internal ID number into the Internal ID field of the
Aliquots record. This makes it possible for us to "match up" (relate)
Sample information to Aliquot information (figure a).
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Database Relationships
In Freezerworks tables we have the following relationships - parent,
child, grandchild:
One Sample ID (parent) can relate to many Aliquots (children).
One Aliquot (child to the Sample ID) can relate to many Transactions
(children to the Aliquot and grandchildren to the Sample ID).
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