Annotations, defined

A two-dimensional slice may be taken either parallel to one of the principal co-ordinate planes (X-Y, X-Z and Y-Z) selected from a menu, or in any arbitrary orientation defined on screen by the user. Once a slice through the data has been taken, and displayed on the screen, a number of tools are available to assist the operator with making measurements of indications. These tools allow measurement of distance between two points, calculation of 6dB or maximum amplitude length of a flaw, plotting of a 6dB contour, and textual aimotation of the view. Figure 11 shows 6dB sizing and annotation applied to a lack of fusion example. 

Research into so-called ontologies is also currently very active. Ontologies can be used to characterize the principal concepts in a particular discipline and how they relate one to another. Many people believe they are necessary if database annotation is to be made accessible to both people and software, but also in facilitating more effective and efficient data retrieval. The well-known Gene Ontology consortium, or GO, defines the term ontology as ... specifications of a relational vocabulary . In other words they are sets of defined terms like the sort that you would find in a dictionary, but the terms are networked. The terms in a given vocabulary are likely to be restricted to... 

Figure 15 Annotated 60 Hz HSQC-1,1-ADEQUATE spectrum of strychnine (45) showing the, 3C- 3C connectivity network that defines the central "core" of the molecule as shown in grey by 46. Correlations from methylene carbons are inverted and plotted in grey correlations from methine carbons have positive intensity and are plotted in black. There are no methyl correlations, which would also have positive intensity. Adjacent carbons are defined by solid black lines perpendicular to the diagonal. Dashed horizontal black lines define correlations to adjacent protonated carbon resonances, for example, C15 (26.4 ppm) to C16 (60.3 ppm). Dashed curved lines define correlations between adjacent protonated and non-protonated carbons. These responses, in contrast to those between adjacent protonated carbons, are not diagonally symmetric. Responses enclosed in black boxes are artifacts that arise from the overlap of H14 and one of the anisochronous Hll methylene proton resonances.

In 1965 Seshardri et al. described the isolation of an unknown terpenoid acid B obtained from the lichens of Lobaria retigera in the western Himalayas [8]. (Note that this annotation bears no relation to the subsequent nomenclature later defined by Corey and Shibata.) Four collections had been made in the summer of 1962 from under the Rutba plants in the Valley of Flowers (12,500 feet) and on the way to Hemkund Lokpal (13,500 feet) and from underneath rocks and from pine trees in Ganghariya (10,000 feet). The samples were subjected to a series of increasingly polar extractions (petroleum ether, diethyl ether, acetone). The unknown terpenoid acid B was present in all petroleum ether extracts, except that of the sample obtained from the Valley of Flowers, in compositions ranging from 0.47 % to... 

The emphasis in design shifts to the responsibilities of the instances of each class (or larger component). Each class has a defined purpose for its existence that determines which operations and information should reside in its instances. This purpose should be documented succinctly in the annotation of a class. A standard rule of thumb is that better designs have classes that can be more briefly described. 

Under this framework. Fig. 6 shows the basic pieces for constructing annotated chemical libraries. On the one hand, proteins should be stored using the appropriate annotation under their respective protein-family classification schemes (in this case, nuclear receptors). On the other hand, molecules should be stored using a unique hierarchical identifier. The link between the two entities (molecules and proteins) would be defined by pharmacological data (activity). The use of a certain criteria would then allow to construct a binary annotation matrix, from which the mapping of the chemogenomic space is established. 

In addition to fragment and graph indexing of polymer information, the POLID-CAS YR system also makes use of two distinct vocabularies for non-structural terms. The first vocabulary is, in essence, a controlled vocabulary of hierarchically ordered terms (taxonomy), supplemented by a second, more fluid vocabulary, which is subject to constant editing. The latter is used to further enhance the controlled vocabulary, e.g., the term isomerization , which is part of the controlled vocabulary, could be defined further by the terms racemization , tautomerization or rotation isomerization . Annotation of this kind is only a short step away from techniques, which we now associate with the terms tagging and folksonomies and which are typical components of Web 2.0 systems. POLIDCASYR s controlled vocabulary is structured according to a number of semantic categories such... 

One way to impart structure to otherwise unstructured documents is to utilize a suitable markup language. The function of markup languages is to combine the text of a document with further information about the text (markup languages typically add metadata - data about data) and while metadata is normally hidden from the view of a human reader, it is available to processing software. XML allows an author to add arbitrary metadata to documents through the use of tags, which are user-defined and annotate data sources. 

Fig. 14.6. Annotations for inhibitors that bind to unactivated kinase conformations. Sorafenib binds to the DGF-out conformation and its core is defined as Bayer like dfg. PD318088 binds to the aC-Glu-out conformation and its template is MEK like 3.

Fig. 16.8. Reactant-level (pre-enumeration) design steps. This is a screen shot of PGVL Hub during the design of the two libraries. The reactant sets for this two-component reaction and the generated explicit libraries and products are all captured during the design session (see the left-hand side). The -component is for acids and the B-component for amines. The molecular structures of the two special acids are shown in Fig. 16.6. Many annotations can be added to reactants to aid their analysis and selection. Here ClogP, molecular weight (MW), similarity (SIMI) with respect to a user-defined reactant, and reactant amount available in the inventory house are just a few examples.

Annotate The type (text, intensity, ppm, Hz or points) and the font, type and color for annotation may be defined. 

Chemical species reside within phases, as defined generally above. We define three broad types of species gas phase, surface, and bulk. The first type is a species in the gas phase, which might be annotated in a reaction by (g). The number of gas-phase species is denoted... 

Any species in the solid below the gas-solid interface, is defined to be a bulk species. Chemical names of species in bulk phases might be annotated by (b). Each bulk phase must have at least one bulk species. A bulk phase with only one species is considered a pure bulk phase one containing several bulk species is considered a bulk mixture. The number of species in bulk phase n is termed Kb(n), and the species in that phase are numbered sequentially from the first species in the phase k[(n) to the last species Klb(n). The total number of bulk species in all phases is designated Kb. When we have accounted for all of species in the mechanism (gas + surface + bulk), the total number is... 

However, it is clear that the ease of collecting proteome data currently exceeds the capacity to analyse it. Therefore, international standards are being sought for proteomic experiments, such as the proteomics standards initiative (PSI, http //psidev.source forge.net/), and the proteomics experiment data repository (PEDRo, http //pedro.man.ac.uk). The aim is to provide proteomic researchers with the opportunity to query and reproduce protocols, analyse raw or metadata from other laboratories, and to link the proteome with the respective transcriptome and the metabolome. The Human Proteome Organization (HUPO) is establishing a defined infrastructure for human data submission, and annotation for the numerous proteomic data platforms. This will also be required to effectively develop parasitic flatworm proteomics. 

From genome sequences, a plethora of DNA sequence information is, often publicly, accessible in databases. Pieces of genome sequence have often been annotated, based on sequence similarity to other genes with similar function, to possess a certain function. From the gene sequence, the corresponding protein sequence of a putative enzyme can of course be readily derived so that at this stage the target of the search for a new enzyme is defined. 

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