Annotations manual

A new tool for computational ADME/Tox called MetaDrug includes a manually annotated Oracle database of human drug metabolism information including xenobiotic reactions, enzyme substrates, and enzyme inhibitors with kinetic data. The MetaDrug database has been used to predict some of the major metabolic pathways and identify the involvement of P450s [78]. This database has enabled the generation of over 80 key metabolic... 

SwissProt (http //www.expasy.org/sprot), database established by the Swiss Institute of Bioinformatics, provides protein sequences with high level of annotation. Highly integrated with other protein databases. All data are verified manually. 

SPTR has been produced weekly since its start in January 1998. At the 14.6.1999, SPTR contained 323,354 entries 79,449 SWISS-PROT entries, 201,065 TrEMBL entries, and 42,840 TrEMBLnew entries. As the rate of incoming data and the addition of value through manual curation and automatic annotation increase, the plan is to produce SPTR daily in the near future. 

Matador http / / matador.embl.de A manually annotated database linking drugs to targets. 

Fig. 4.13 Display and button panel in the Multiplet mode with the Report Multiplets dialog box and the box for manual connection and annotation activated.

The definition of pharmacophores is done manually by applying so-called schemes using a Pharmacophore Query Editor. A template molecule is generally used for this purpose. In the MOE environment, a scheme is a collection of functions that define how each ligand is annotated. This is accessed via an SVL function. The default scheme is called PCH (Polarity-Charged-Hydrophobicity). New schemes can be created to represent certain molecules better, e.g. Planar-Polar-Charged- Hydrophobiaty [91]. 

Because licensed vaccines are the focus of much attention in the public as well as in the vaccine research community, VIOLIN has two subdatabases that focus on licensed human and animal vaccines. The Huvax subdatabase (http //www.violinet.org/huvax) stores all licensed human vaccines in the USA and Canada. The data for these licensed human vaccines are annotated through manual curation and a vigorous review process. Huvax includes manually curated data including manufacturer, trade name, storage information, age at which the vaccine should be administered, and other relevant information. These vaccines are also listed by the CDC CVX codes (codes that indicate the product used in a vaccine) for tracking vaccination records. Huvax has provided cross-references based on these CDC CVX codes. Huvax provides ways for users to search, compare, and analyze licensed human vaccines. Various criteria can be used for querying human vaccines. Different vaccines can also be compared side by side. Vevax is a VIOLIN database of licensed veterinary vaccines (http //www. violinet.org/vevax). 

Matyska L, Juhova K, Mikula P, Potucek V. Kratochvil M (1990), The Program Package PEGAS I. Manual, II. Annotated Examples, Organic synthesis and computers vol 9. Dum techniky CS VTS, Pardubice... 

The UniProt KB is an automatically and manually annotated protein database drawn from translation of DDBJ/EMBL-Bank/GenBank coding sequences and directly sequenced proteins. Each sequence receives a imique, stable identifier allowing unambiguous identification of any protein across datasets. The KB also provides cross-references to external data collections such as the underlying DNA sequence entries in the DDBJ/EMBL-Bank/GenBank nucleotide sequence databases, 2D PAGE and 3D protein structure databases, various protein domain... 

HPRD www.hprd.org/ Licence for commercial user Human proteome annotation database including 33,000 manually curated Human protein interaction Peri et al. (2003)... 

A manually annotated database called MetaCore has been developed and consists of... 

If no rule could be selected automatically, the user has to decide which rule is to be executed. Therefore, in the next step (find decisions), all conflicts are collected and presented to the user. For each half link, all possible rule applications are shown. If a rule application conflicts with another rule of a different half link, this is marked as annotation at both half links. Rules that are not executable due to a missing context are included in this presentation but cannot be selected for execution. This information allows the user to select a rule manually, knowing which other rule applications will be made impossible by his decision. The result of the user interaction (ask for user decision) is stored in the graph and the selected rule is executed in the execution phase. 

Manual annotation experience shows that it is often advantageous to take into account all available information to improve gene identification. Auto-... 

Nucleotide Sequence Database [26]) steps in. TrEMBL was created in 1996 and consists of computer-annotated entries in SWISS-PROT-like format. It is populated by protein sequences translated from the coding sequences (CDS) in EMBL and is a supplement to SWISS-PROT. In a way, it can be considered as a preliminary section of SWISS-PROT indeed, once the manual annotation is performed, the entries move on to SWISS-PROT. 

---