1. Object orientation: What is an object in Biology and what “methods” can biological objects in execute? Provide at least three examples for “methods” executed by bio-objects.
An object in biology is a class of biomolecules that has specific attributes and the ability to execute certain methods.
DNA, RNA, Proteins, Lipids and Sugars (Carbohydrates) have different methods as “Bio-Object”s.
-DNA has methods such as
1) strand separation
2) replication
3) packaging in chromatin
4) Re-association / hybridization
-RNA has methods such as
1) interaction with ribosome
2) recognition of other RNAs
3) Re-association / hybridization
-Protein has methods such as
1) interaction with other biomolecules
2) enzymatic functions
3) structure functions
4) transport functions
-Lipids has methods such as
1) interaction with other biomolecules
· e.g. association to form biomembranes
· e.g. binding (covalent and non-covalent) to proteins
-Carbohydrates has methods such as
1) interaction with other biomolecules
· polymerization
· conjugation (chemical reaction)
2. What are typical attributes of Nucleic Acids? Name at least three of them!
· Sequence
· Secondary structure
· Patterns and motifs, binding sites for proteins
· Chemical stability(RNA)
· Packing in chromatin(DNA)
3. Which categories of biomolecules do you know?
Categories of biomolecules:
· Proteins
· Nucleic acids
· Lipids
· Carbohydrates
· Small molecules (Metabolites, …)
4. Which categories of bioDATABASES correspond to these categories of
bioMOLECULES?
bioMOLECULES?
Biodatabases are libraries of lifescience collected from experiments and publications in various biological areas.
Nucleic acid
Primary sequence databases
Protein
Protein-protein interaction
Carbohydrates and lipids
Lipid, Small Molecules
5. Please give at least one example for each category of biodatabase as we see them categorized at the EBI SRS interface
1) Literature, Bibliography and Reference Databases – MEDLINE, OMIM, Karyn’s Genomes etc.
2) Gene Dictionaries and Ontologies – UNILIB, GO, HGNC, UniGene, ENTREZGENE, SO(Sequence ontology) etc.
3) Nucleotide Sequence Databases – EMBL, RefSeq Genome, Patent DNA, Genome Reviews etc.
4) Nucleotide Related Databases – TRANSFAC, TRANSCELL TRANSSITE, TRANSGENE.
5) UniProt Universal Protein Resource – UniProtKB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, UniRef100, UniRef90, UniRef50, UniParc
6) Other Protein Sequence Databases – Patent Proteins, EPO Proteins, JPO Proteins, RefSeq Proteome etc.
7) Protein Function, Structure and Interaction Databases
· Function – PEP (ORFs), InterPro, PROSITE etc.
· Structure – PDB etc.
· Interaction – Experiment, Interactor, Interaction
8) Enzymes, Reactions and Metabolic Pathway Databases – LENZYME, ENZYME, UPATHWAY, UREACTION etc.
9) Mutation and SNP Databases – HGVBASE
6. Which major portals to biodata do you know?
· SRS (Sequence retrieval system)EBI (European Bioinformatics Institute)
· ENTREZ for NCBI (National Center for Biotechnology Information)
· ExPASy (Expert Protein Analysis System) for SIB
7. What sort of discrepancy exists between biodatabases that represent information on genes & genomes as opposed to biodatabases that store information on gene expression?
Genes and genome databases cover sequence information that should be identical in every cell and under every condition of the analysed organism. Opposed to that, information stored in databases about gene expression may vary due to the analysed tissue or the experimental conditions and thus also covers information about the actual experiment the data came from. They can also give insight to the function and regulation of genes through information on gene expression levels under certain conditions.
8. What is a “flat file database”?
A “flat file database” describes any various means to encode a database model (most commonly a table) as a single file. It is a relatively simple database system in which each database is contained in a single table, which usually contains one record per line and where the single fields can be separated by delimiters.
9. What features would you assign to “Bioinformatics” and how does it differ from “Systems Biology”?
Systems biology is a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems and how these interactions give rise to the function and behavior of that system.While Bioinformatics is the application of computer technology to the management of biological information.
Hence, while bioinformatics takes an exhaustive approach wherin where all information obtained biological sample (such as biomolecule sequence, their structure and interaction) is stored electronically and most of it is analyzed further. System biology however deals only with studying how different biological infrormation merge to perform as a system.
10. Annotate a sketch of biomolecules with entity-types from biodatabases you know.
The biomolecules are given with the following entity types is Bio-databases:-
DNA and RNA and proteins: Sequence, sequence length, organism name, taxon etc.
Carbohydrates and lipids: Molecular structure, Mass, Nomenclature etc.
11.How are BioDatabases integrated in SRS? What does the SRS documentation say about the mechanisms used for linking between biodatabases? (http://srs.ebi.ac.uk/srs/doc/index.html)
A databank entry may contain references to other databanks, and vice versa. In SRS these relationships are known as links and can be used to extend a query across multiple databanks. Thus you can obtain all the entries in one databank that are linked to an entry (or entries) in another databank.
From a user perspective there are two types of link: hypertext links and index links (query links).
Hypertext links are links between entries which are displayed as hypertext. These are hardcoded into SRS and you can use them whenever you wish. They are useful for examining entries that are referenced directly from entries.
Index links are built into the SRS indices at the same time as databanks are added. They allow you to construct queries using relationships between databanks. They require SRS to search through entries or indices in other databanks, looking for matches.
12.What does “computer readable knowledge” mean?
The knowledge that is characterized by computer, which contain a set of data, often in the form of rules that describe the knowledge in a logically consistent manner and so that can be understood both by human and computer.
For example if we are dealing with Biodatabses then in this context the computer readable knowledge will mean that it should have proper set of Ontologies and Controlled Vocabularies which can be understood by the databases and reffered to in various others too.
13.The EBI call itself “the portal to knowledge”. How is biomedical knowledge
represented in biodatabases?
Biomedical knowledge is represented in different biodatabases: Such as OMIM, MEDLINE, MeSH, and PubMed. OMIM is a review focusing on diseases, their phenotypic appearance, and genes related to their etiology. MEDLINE is the largest part of the PubMed and contains freely accessible online biodatabases of biomedical journals, citations, and abstracts created by NLM. PubMed contains Medline and other citations from other sources of biomedical journals. And finally, the MeSH thesaurus is used by NLM for indexing articles from biomedical journals for the MEDLINE®/PubMED® database.
14.In one of the links to “relevant background information”, a primer on molecular
biology mentions “linkage disequilibrium”. What does this term mean?
Linkage disequilibrium describes a situation in which some combinations of genes or genetic markers occur more or less frequently in a population than would be expected from their distances apart.
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