Databases submission process

The Local sequence identifier is most prominently used in the data submission tool Sequin (see Chapter 4). Each sequence will eventually get an accession, version identifier and a gi number, but only when the completed submission has been processed by one of the public databases. During the submission process, Sequin assigns a local identifier to each sequence. Because many of the software tools made by NCBl require a sequence identifier, having a local Seq-id allows the use of these tools without having to first submit data to a public database. 

The submission process is governed by an international, collaborative agreement. Sequences submitted to any one of the three databases participating in this collaboration will appear in the other two databases within a few days of their release to the public. Sequence records are then distributed worldwide by various user groups and centers, including those that reformat the records for use within their own suites of programs and databases. Thus, by submitting a sequence to only one of the three major databases, researchers can quickly disseminate their sequence data and avoid the possibility that redimdant records will be archived. 

Proteins include the enzyme molecules that carry out many of the biological reactions we study, and their sequences are an intrinsic part of the submission process. Their importance, which is discussed in Chapter 2, is also reflected in the submission process, and this information must be captured for representation in the various databases. Also important are the protein product and gene names, if these are known. There are a variety of resources (many present in the lists that conclude these chapters) that offer the correct gene nomenclature for many organisms (cf. Genetic nomenclature guide, Trends in Genetics, 1998). 

First conceived at a conference sponsored by the CoML, in its first 10 years, the achievements of OBIS were remarkable it amassed nearly 20 million records within 600 separate databases. Currently, it is home to nearly 40 million records. To ensure its continuing success and expansion, OBIS has simplified the submission process, and now provides a simple Microsoft Excel template on which data can be submitted. 

All the sections must be completed by the user and then submitted to a single administrator for addition to the database. Upon completion of the form, the user has the option of making a check submission, which processes the data and performs error checks as normal, but displays the verdict on screen for the user rather than sending the data to the administrator. A variety of errors are checked, including missing data and inconsistent data, invalid molecular structures or numeric data outside the normal range. When the user is satisfied with the form data, they can be submitted to the administrator via the exporf button. Upon submission, the data are stored... 

In the US the FDA request within the submission an electronic version of the database and this gives them the opportunity to not only re-analyse the data to confirm the results presented within the submission, but also to perform their own alternative analyses. This does not happen in Europe. In the US, therefore, the process following submission is somewhat different and much of the interchange in terms of requesting and supplying alternative analyses is taken care of by the FDA statisticians. 

When a compound arrives at the compound management operation, the initial information must be verified and recorded in an inventory database. First, the sample must be associated with its container. This means a unique container identifier such as a barcode must be assigned to the sample. The container must carry the identifier throughout its lifecycle. Then initial data about the sample must be recorded. This includes the initial amount (weight for solid samples and volume for liquid solutions), concentration if in solution, container data such as barcode, type, and tare weight (if weighing will be part of the dispensing process). Submission creates or initiates the record of the container in the inventory. 

To begin to save a record, press the Bankit button again. The view that now appears must be approved before the submission is completed that is, more changes may be made, or other features may be added. To finish, press Bankit one more time. The final screen will then appear after the user toggles the Update/Finished set of buttons and hits Bankit one last time, the submission will go to NCBI for processing. A copy of the just-finished submission should arrive promptly via E-mail if not, one should contact the database to confirm receipt of the submission and to make any correction that may be necessary. 

The World Wide Web site of the Protein Data Bank at the RCSB offers a number of services for submitting and retrieving three-dimensional structure data. The home page of the RCSB site provides links to services for depositing three-dimensional structures, information on how to obtain the status of structures undergoing processing for submission, ways to download the PDB database, and links to other relevant sites and software. 

The available database to assess the safety of ASC and its residues chlorite and chlorate has limitations, and few of the studies have been conducted to the current standards expected for regulatory submissions. The studies on ASC related to a germicidal product, and some of these involved parenteral administration. The Committee considered that although not directly relevant to oral exposure, these studies provided useful supplementary information that did not raise concern about the use of acidified chlorite as a processing aid. In many of the studies in which chlorite or chlorate was administered in drinking-water, the information provided was insufficient to derive an accurate estimation of the dose received by the animals. 

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