| what are secondary databases? | make use of publicly available sequence data in primary databases. |
| what are some bimolecular databases? | UniProt ,ExPASy |
| how is UniProt structured? | n |
| what is UniProt and what does this database consist of? | UniProtKB Translation of EMBL coding sequences , UniProtKB/Swiss-Prot section (reviewed) which is annotated by experts and has high amounts of info, The rest (90% of the entries). |
| what are some of UniProts features? | The most comprehensive protein database in the world,Annotation by experts: annotators are specialized for different types of proteins or organisms with huge team,World-wide recognized as an essential resource. |
| what is ExPASy? | Expert Protein Analysis System |
| what are some 3D structure of macromolecules databases? | Worldwide Protein Data Bank and The Protein Data Bank (PDB ) |
| what are the 4 protein banks that comprise the World wide protein data bank? | Biological Magnetic Resonance Data Bank (BMRDB), Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), PDBj, and PDBe. |
| what is the genome databases used in (comparative genomics) | EnsemblGenomes (access to complete genomes and proteomes) |
| what are the databases for protein domains? | Prosite and CATH. |
| what does the Prosite database align sequences and logos? | the sequences that are used to built the Prosite profile,The Sequence Logo indicates the level of conservation of each residue. |
| what is the domain signature in the Prosite database? | The domain signature is a string-based pattern representing the residues that are characteristic of a domain. |
| what is CATH database? and how do they cluster proteins? | is a hierarchical classification of protein domain structures, which clusters proteins at four major levels:
❑ Class (C),
❑ Architecture (A),
❑ Topology (T)
❑ Homologous superfamily (H). |
| How are the CATH boundaries and assignment for each protein determined? | using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis. |
| what does Ontology mean? | Ontology (information science)is the philosophical study of being, is a way of showing the properties of a subject area and how they are related, by defining a set of concepts and categories that represent the subject. |
| how to answer the problems of inconsistencies in the annotations? | by Controlled vocabulary,Hierarchical classification between the terms of the controlled vocabulary. |
| what are the gene ontology processes? | DNA metabolism ( DNA, repair, replication,packajing,recombonation) |
| what are the gene ontology molecular functions? | nucleic acid binding and enzymes. |
| what are the gene ontology cellular components? | nucleus and cytoplasm. |
| what's the gene ontology database ? | The Gene Ontology (GO) database is a resource for ontological information. |
| what is the status of GO annotations? | Term definitions (biological processes, molecular functions, cellular components, sequence ontology), Genomes with annotation (excluding annotations from UniProt) ,Annotated gene products. (total, electronic only, manually curated). |
| what's the quick GO? | A user-friendly Web interface to the Gene Ontology, with Graphical display of the hierarchical relationships between terms that makes in convenient to brows between classes. |
| what are some remarks on "bio-ontologies"? | Improvement compared to free text,Nothing to do with the philosophical concept of ontology (only a taxonomical classification),Multiple possibilities of classification criteria, it should remain purpose-based,No representation of molecular interactions (relationships between objects are only hierarchical). |
| What is biological function? | A general definition,Function: characteristic action (role) of an element (organ) within an set |
| what is the function and gene ontology of biological functions? | Understanding the function requires to establish the link between molecular activity and the context in which it takes place (process). |
| what are the databases that include small compounds, reactions and metabolic pathways? | (KEGG) Kyoto Encycplopaedia of Genes and Genomes , (BioCyc ) Metabolic pathways. |
| how does the function and gene ontology have Multifunctionality? | Same activity can play different roles in different processes, Multiple activities of a same protein in a given process. |
