Source file formats

An issue closely related to logical integration is the use of common file formats and shared languages to communicate information between different data sources. The most common language currently in use is the [11] XML, which is widely used in... 

The generation of the correct compound structures is a critical step in which different components such as atomic valences, correct bond orders and properly defined aromaticity have to be considered carefully. In addition, the correct stereochemistry flags need to be added for a correct treatment of stereochemistry. Most of the current pharmacophore generation packages include compound builders, but users can also import them from external sources using common file formats, for example SMILES, MOL, SD or MOL2. 

Cross-References to Other INDs. At times, IND submissions are supported by a cross-reference to another IND [21 CFR 312.23(b)]. The utility of the electronic IND submission will be further increased if all reference materials are supplied with the IND submission. You should handle these files in the same manner as other electronic files submitted to the IND. For example, you should generate the files from electronic source files rather than from scanned paper documents if at all possible. If the electronic source file is not available, we will accept a scanned copy. You should describe the file format and organization of these files as described in this guidance. 

However, even if we work only with well-defined structures, it is always a good idea to store the source files (usually in the native format of the software that was used to create them), because in this way we can make sure no part of the drawing is lost in the conversion. However, native formats usually have the disadvantage of being bound to one specific program, and options for their automatic processing are limited. For this reason native data should be auxiliary, and the data for everyday use should be stored in some widely supported, well-documented format, probably one of those described above. This approach would also create a future-proof copy of our data, because proprietary formats tend to be problematic to use after 10 years or more. 

The document types that may be stored within the system may have a wide variety of file formats and sources, and range from just key documents to the totality of documents generated for a project. Eor each type of document stored in the EDMS, it is important to define the original version (i.e., as paper or electronic). 

Cleaning and Transforming Data. When importing data from diverse data sources (files, databases, spreadsheets, LIMS systems, etc.) into a database or data warehouse, the 4 ta usually needs to be standardized, checked, and sometimes transformed to some common format and content. This allows faster search and retrieval, and serves as a check of data integrity. The rules that define the cleaning/trans-formation process are often termed "business rules," and in the case of chemical data, they may include checking and modification of chemical structures. 

Users with appropriate system privileges must be able to export documents in their native formats to any local or remote file systems to which they have access. Documents must be available for viewing in a standardized read-only format. Users must be able to view documents even if they do not have the native application. Users must also be able to match a printed or exported document to the original source file within the EDMS by means of unique system-generated identifiers referred to as watermarks. Watermarks must not obscure any information on the document and must be in a standardized format. Watermarks must not be obscured when the document is bound. 

Although a traditional publishing process was used in the creation of the first two editions of AMH books, the need to provide users with multiple formats has required the work environment to be re-engineered and editors now work in an SGML environment. This allows production of reports such as a print-ready file (from which the book is published) an HTML version that serv es as the current CD-ROM and web-based products and potentially other formats or subsets of AMH data, from one set of source files. 

Each row in the coordtest table represents a molecule. The smiles column is a string of atom symbols and bonds and the coord column is an array of atom coordinates. How is it possible to keep the ordering of atoms in the smiles string in sync with the ordering of atom coordinates in the coord array When the coordinates are initially entered from the external source, they are likely to be in a common chemical file format. The program that converts from that file format to SMILES would have to output the atom coordinates in the same order as the atoms in the SMILES. 

There are many programs available to parse the various molecular structure file format. OpenBabel is an open-source program that can read many file formats and produce a SMILES representation of molecular structure. There are many other commercial products that can do this as well. In the following examples, the OpenBabel/plpythonu implementation of molfile parsing will be used. This was introduced in Chapter 10. The code to define the necessary functions is shown in the Appendix. 

All three programs store the input information on floppy disk. Most of the input is done by external contributors who send the disks in certain time intervals to our institute for further processing. The data of the different input sources are uploaded into our IBM mainframe computer, converted to the same file format and stored in an intermediate file. After several additional automatic and manual checks the data are loaded under the database management system ADABAS (Figure 4). 

Acquisition of Spectra sample source sample purity sample preparation spectrometer type spectral resolution additional data possible (e.g., special sample conditions file format)... 

In 2012, the standard PDF/A-3 (ISO 19005-3 2012) has been released, which allows to save the original source files, for example, XML, CSV, XLS, DOC, CDF, CAD, JPEGS, together with the long-term archiving enabled PDF/A format... 

Format of Source File and Quality Trimming of Raw Sequence Reads... 

The ELBT.EXE program on the CD-ROM allows the fast search of data according to property type, chemical system (substances, mixtures, and solutions), and reference (authors, original source of data, and year of publication). The program displays the data tables for all the 3316 systems as PDF files, in the same format as in the book. The totality of numerical data points is also displayed by the program in two computer readable standard ASCII file formats, SELF and ELDATA. Estimated uncertainties are... 

Sonic Foundry Perfect Clarity Audio (. pca) is another proprietary format from Sonic Foundry. This is a newer and more advanced format that compresses files losslessly. This means that the file size of a. pca file is considerably smaller than standard uncompressed file formats while retaining 100 percent of the original file quality. For audio files that will remain on your computer, this is an excellent choice, since you can save disk space without sacrificing quality. Use caution when distributing. pca files to others, because they won t be able to use them unless they have Sonic Foundry software installed. The amount of lossless compression depends on the complexity of the project and the source media used, but it can typically result in a file-size savings of 30 percent or so. 

A perpetual thorn in the flesh of any modeler who uses multiple programs from multiple sources, be they in-house or commercial, is the lack of compatibility between the different file formats used by the various programs. Despite efforts to move toward a standard, multiple and incompatible formats still proliferate. Some relief is provided by file format conversion programs such as BABEU and MOL2MOL. Many proprietary utilities for this purpose also exist (e.g., Convrt o ). 

The formatting of a database involves the creation of several types of files that are manipulated with specialized software. A source file containing raw analytical data is converted to a library file by reducing noise, eliminating unimportant data and compression. Associated exchange files enable data to be transferred in a standard format such as JCAMP/DX for spectrometric data and JCAMP/CS for chemical structures. 

The standardisation process is broken. Standards need to be open source to facilitate easy updating in a highly volatile profession, and of unlimited free access. Proprietary file formats have caused enough misery without compounding it with proprietary standards. The current situation whereby standards are heavily protected, expensive and frequently outdated before they even appear is unhelpful to say the least and it is possible that Wikipedia and its like may play a substantial future role. NASA also has always been an excellent role model here, providing free access to lots of useful documents and data (e.g. Dvorak 2009). However, on a cautionary note, open source standards without measurement constraint will simply produce free words. 

MOPAC nms in batch mode using an ASCII input file. The input file format is easy to use. It consists of a molecular structure defined either with Cartesian coordinates or a Z-matrix and keywords for the type of calculation. The program has a very versatile set of options for including molecular geometry and symmetry constraints. Version 6 and older have limits on the size of molecule that can be computed due to the use of fixed array sizes, which can be changed by recompiling the source code. This input format allows MOPAC to be run in conjunction with a batch job-queueing system. 

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