Common exchange data format

This is fundamental to the progress of genomics (and many other areas) of science. Generating data in a common exchangeable format, with a common lexicon of terms [47] in a single non-redundant location is a major goal. A number of examples exist, such as the DNA and protein sequence data in GenBank, EMBL or SwissProt [48-50]. 

BioPAX (http //biopax.org/), the group developing a common exchange format for biological pathways data, uses OWL. BioPAX can capture molecular binding interactions and manage small molecules (represented by InChl). Another example of RDF usage in chemistry is provided by the CombeChem project (Taylor et al. 2006). 

A full release of GenBank occins on a bimonthly schedule with incremental (and nonincremental) daily updates available by anonymous FTP. The International Nucleotide Sequence Database Collaboration also exchanges new and updated records daily. Therefore, all sequences present in GenBank are also present in DDBJ and EMBL, as described in the introduction to this chapter. The three databases rely on a common data format for information described in the feature table documentation (see below). This represents the lingua franca for nucleotide sequence database annotations. Together, the nucleotide sequence databases have developed defined submission procedures (see Chapter 4), a series of guidelines for the content and format of all records. 

Schramm, T., Hester, A., Klinkert, I., Both, J.-P., Heeren, R Brunelle, A., Laprevote, O., Desbenoit, N., Robbe, M.-F., Stoeckli, M Spengler, B., and Roempp, A. (2012) imzML-a common data format for the flexible exchange and processing of mass spectrometry imaging data. ]. Proteomics, 75, 5106-5110. 

A multitude of processes exists that benefit from neutral based data exchange of CAD data in engineering-related domains. Based on live typical use cases an analysis of common neutral 3D formats was done [8]. The four engineering formats STEP, 3D XML, JT and 3D PDF were reviewed and assessed for their suitability for the following application scenarios ... 

ODB++. The ODB++ data format is a common language used for DEM and CAD/CAM data exchange. It overcomes many data communication obstacles within design/manufacturing supply chains. Data in this powerful open database impart an integrated and accurate physical model of all bare-board, component, and test-related information. It is designed as a simple yet comprehensive description of all entities used in the manufacture and assembly of a PCB. 

The layout editor may have an internal data format that is used to store the layout, and it should also be able to generate output data files in the formats that are commonly used by foundries. These include GIF (Caltech Intermediate Format) and GDSII (Graphic Data System). Some tools do not support these formats, but it may be possible to find eon-verters from one file format, such as DXF (Drawing Exchange Format), to the required format, such as GDSII. Typically the user will transfer the data file to the foundries mask data folder using an FTP (file transfer protocol) command. In some cases the foundry may require the user to submit checksum data to ensure that the file transferred eorrectly. 

Spreadsheets as data representation format are often used to share, store, and exchange data in engineering enviromnents despite of a set of important drawbacks, such as the implicit data schema hampers automatic and effective processing high-level of freedom and, therefore, high variabUity in data representation, which often does not adhere to best practices of data representation. These weaknesses are balanced by the positive characteristics of spreadsheets. Indeed, from a user point of view, spreadsheets are easy to understand, they do not require sophisticated skills to create and work with and have adequate representational power and expressiveness for many common tasks. 

A second way of looking at chemical representation is to consider the manner in which the chemical structure data is organized and exchanged, either in some file format or in a database. The most common ways of representing structures and reactions include the following. 

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