all right so
now i'll take a color and it's time to
discuss
more
about biological databases okay so
biological database okay short form of
database db that's what we write
okay
so
what are databases we have been using
this term for a long time now we know
that databases are
what electronic uh what i can say
electronic is this is analogy like a
dryer you know in drugs we can organize
thing so just like an electronic dryer
or cabinet system where we can store our
data okay
and we can retrieve those data whenever
we need them
whatever kind of so for different
specific type of data we have specific
database for open reading frame data we
have orf database for single nucleotide
polymorphism data we have snp database
so we have different kinds of database
for example the database for for
proteins also there are structural
database there are sequence database
sequence database is the one from where
we get the sequence of the primary
sequence of proteins and structural
databases where we get the topology of
the proteins
like that okay so what are some common
biological databases
and their types so the very first and
very common type is a nucleotide
database
nucleotide sequence
database nucleotide sequence database
that contains genes
and also genome
okay genes and genomes both
then what we have we have protein
databases protein sequences
protein
sequence in the database form
okay
then what we what else we have
we have macromolecule structures
macromolecules particularly the
structure like carbohydrates proteins
lipids all this what else we have
we have a protein protein interaction
very important to understand the protein
protein interaction to study the
pathways
those databases are there
we also have
so let's write metabolic pathways
okay so there are
different types of numerous metabolic
pathways continuing inside of a cell and
we have database for that
we also have database for gene
expression and profiling
gene expression database and we also
have literature
literature
okay example of literature we have
already talked about pubmed is an
example
and there are books available in some
places but these are the database that
carry information okay so database carry
information and there is a way
so let me take a green color here there
is a way to put the data in
so feeding the data in
and there is also a way to take the data
out or extract the data
okay
so data feeding or input
as well as extract both are possible
okay
and the amount of data that we're
dealing with it's increasing day by day
with
increasing a number of experiments on
specific topics the data set that we are
expecting is also to be increased okay
it's increasing every single day
so what we are getting from here is that
huge amount of data
beat nucleotide sequence protein
sequence
macromolecule structure protein protein
interaction all these different kinds of
data
and this data need to be placed
somewhere in this database there is a
way to put the data in there's a way to
extract it we have discussed it earlier
as well
but for
forming a biological database
it must carry it must have some feature
a must have feature there are two must
have two must have what you can say two
must
have
features are needed
two must-have features are needed what
are those
one is non-redundancy
non
redundancy now what is this
now there should not be any redundancy
or if there is a redundancy the value of
redundancy is very very low that means
whenever we put something into this
database
okay it occurs only once
means there should not be any duplicate
entry
in the same database so
no
duplicacy
or you can say no duplicate
entry
when we are putting the information in
there must not be any duplicate entry
that is called non-redundancy
now we try to minimize this redundancy
to as low as possible non-redundancy is
the criteria that we want to achieve but
it's not possible always so we always
try to go with a low very low redundancy
near to non redundancy
this is very first feature the second
important feature
sharing of the data
okay
data sharing protocol
so basically the database is what it's a
reserver of data
reserver of experimental data scientific
data which is actually gathered and
stored for the use of science itself for
the for the use of exploration of the
science itself okay for examination
inspection
so basically this sharing of the data is
important it means that if this is the
database for example the network of data
data is inside
and we said the data is locked
the data is locked you cannot access the
data you can see the data but you cannot
modify if the data has some mis
information or any
mistakes
that should not be a scientific idea
that is a non-scientific idea and
science is progressive it always
explains things from different angles
and also the thinking is progressive so
we can say that in database whatever
data is present the data must be
available for sharing so that we can
examine the data we can inspect the data
and so there is no there shouldn't be
any locked data the data must be free to
deal with
because let's say there are few
scientists a group of 30 scientists 30
researchers they put some data in the
database
with a dna sequence for example
a dna sequencing data and then later
after five years some other group of
scientists and researchers are doing the
same work they are working with the data
they find something
wrong about the earlier data so they can
update it there should be room to do
that that is data sharing okay
so what we can tell about a database is
a collection of data which is normally
structured
searchable
updatable periodically
that is known as a database
so reserver of biological data but which
is more structurally organized
which is searchable
and which is updated periodically
will be termed as a progressive
biological database or simply as a
biological database
got it
this is what biological database is
now let's talk about the classification
of biological database
biological database classification
there are different types of database
okay so let me give you an idea about
the database types here we have sequence
database
sequence database i am writing short
form db means database okay
then we have structural database
structural
database and what else we have 3d
structure base
you