Arena3D

  Visualizing biological networks in 3D

Input File Description

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 EMBL, Meyerhofstrasse 1,
 69117 Heidelberg,
 Germany
 Room:: V116
 Tel:: +49 6221 387- 8140

 Author - Developer
 Georgios A. Pavlopoulos
 pavlopou@embl.de

 Scientific supervisor
 Reinhard Schneider
 rschneid@embl.de
 Arena3D

 

 Input File   -   Example   1

1.     #-----------------------------------

#Here is the number of layers

#-----------------------------------

number_of_layers::4

#-----------------------------------

#Here are the elements of each layer.

#No duplicated names are allowed

#-----------------------------------

layer::pathways

A

B  URL::www.gmail.com

C  URL::www.google.com

D

E

F

end_of_layer_inputs

#---------------------------------------

layer::chemicals

A

B

C

end_of_layer_inputs

#---------------------------------------

layer::diseases

A

end_of_layer_inputs

#---------------------------------------

layer::proteins::clustering=false

A

B

C

end_of_layer_inputs

#---------------------------------------

#Here are the connections between #different layers

#Name of the element::number of layer \t #weight of the connection

#---------------------------------------

start_connections

A::pathways              A::chemicals   1

A::pathways              B::pathways    0.03

A::pathways              C::pathways    0.04

B::pathways              C::pathways    0.05

A::pathways              D::pathways    1

A::pathways              E::pathways    1

A::pathways              F::pathways    1

B::pathways              A::chemicals   1

C::pathways              A::chemicals   1

D::pathways              A::chemicals   1

E::pathways              A::chemicals   1

F::pathways              A::chemicals   1

#---------------------------------------

C::chemicals      A::diseases    5

B::chemicals      A::diseases    1

#---------------------------------------

A::diseases       A::proteins    1

A::diseases       B::proteins    1

A::diseases       C::proteins    1

#---------------------------------------

end_connections

#---------------------------------------

 

 

1-8. Whatever is followed after the # symbol is considered as comment and it is not readable by the program.

 

4. Here the user can define the number of layers (4 layers)

 

9. After the tag layer comes the layer name and then the Boolean value if the nodes on this layer will be clustered or not. This tag optional. Here we have the layer with name “pathways” and the nodes will be clustered.

 

10-15. Between lines 10-14 the node names that will be in this layer are given. This layer contains the nodes with names A, B, C, D, E, F. The URL address next to the node name is used in case the user wants to load this web page every time he visits the node. The URL name and the node name are tab delimited. Duplications of node names are allowed because the program cleans them while loading the input file. Further information about more tags that can be supported is given below.

 

16. The label “end_of_layer_inputs” defines that the input for this layer has stopped.

 

19-21. Here is the section of the input of the node names in the second layer. There is no conflict if the names of the node in this layer have the same names of the nodes with another layer.

 

37. The label “start_connections” shows that the data that will follow will describe the connections between the nodes.

 

38-56. The columns in this section are tab delimited. First comes the name of the node and then the symbol “::” and then the name of the layer that this node belongs to. The third column describes the weights of the connection. This weight shows the strength of the connections between two nodes. The value does NOT represent distances but similarities (importance). This can be any value. They are normalized automatically by Arena3D.

 

If there is a connection between A and B and a connection between B and A then the programs holds the first of them. Duplications are allowed because the program cleans up the duplicated connections.

 

Connection weights are not obligatory.

 

 

58. The label “end_connections” shows that the section of setting up the connections has finished.

 

Input File   -   Example   2

start_connections

A::pathways               A::chemicals    1

A::pathways               B::pathways     0.03

A::pathways               C::pathways     0.04

B::pathways               C::pathways     0.05

A::pathways               D::pathways     1

A::pathways               E::pathways     1

A::pathways               F::pathways     1

B::pathways               A::chemicals    1

C::pathways               A::chemicals    1

D::pathways               A::chemicals    1

E::pathways               A::chemicals    1

F::pathways               A::chemicals    1

#---------------------------------------

C::chemicals      A::diseases    5

B::chemicals      A::diseases    1

#---------------------------------------

A::diseases        A::proteins    1

A::diseases        B::proteins    1

A::diseases        C::proteins    1

#---------------------------------------

end_connections

#---------------------------------------

 

 

 

 

 

 

 

 

 

This is a more limited format that is readable by Arena3D. The user has to apply only a list of the connections with their similiarity weights. In this case only the nodes that have at least one connections are visible.


Connection Tagging
FIELD EXAMPLE DESCRIPTION
· TYPE    A::pathways\tA::chemicals\tTYPE::directed This field supports the type of interaction.
· DESCRIPTION A::pathways\tA::chemicals\tDESCRIPTION::This connection is real This field allows description of the connection.
· DETECTED_BY A::pathways\tA::chemicals\tDETECTED_BY::this connection was detected by text mining This field supports some text information about the connection
· LITERATURE_REF A::pathways\tA::chemicals\tLITERATURE_REF::PubMed This field supports some text information about where the connection comes from
· VISIBLE A::pathways\tA::chemicals\tVISIBLE::false If it set to true or skipped then the line is drawn otherwise the correlation is taken into account for the clustering but the line is not shown
· URL A::pathways\tA::chemicals\tURL::www.google.com Every time this connection is shown the predefined link can be loaded into a browser

 


Node Tagging
FIELD EXAMPLE DESCRIPTION
· SYNONYMS NodeName\tSYNONYMS::directed This field supports the type of interaction.
· DESCRIPTION NodeName\tDESCRIPTION::This node has blue color This field allows description of the node. This field supports text information
· KEYWORDS NodeName\tKEYWORDS::chemical, disease, etc. This field supports some text information about keywords that are related to the node
· URL NodeName\tURL::www.google.com Every time this node is selected the predefined link can be loaded into a browser
· CLUSTER NodeName\tCLUSTER::George Arena3D defines pre defined clustering. In this example the name of the cluster is George an the nodes that belongs to this cluster are grouped together.
· URL A::pathways\tA::chemicals\tURL::www.google.com Every time this connection is shown the predefined link can be loaded into a browser


 

 Input File   -   Example   3

number_of_layers::4

layer::pathways    width::10.0  coor_x::20.0       coor_y::0.0  coor_z::22.820919036865234     angle_x::0.0       angle_y::-103.0    angle_z::0.0       color::0.35,0.0,0.0      

a      DESCRIPTION::ougk!       KEYWORDS::key      SYNONYMS::hello    URL::www.google.com      coor_x::-2.177455425262451     coor_y::-1.9459203481674194       coor_z::11.660459518432617     color::0.35,0.0,0.0

b      URL::www.embl.de   coor_x::-2.6378042697906494    coor_y::-2.5       coor_z::11.660459518432617     color::0.35,0.0,0.0

c      URL::www.gmail.com       coor_x::-2.9258646965026855    coor_y::-2.4633395671844482    coor_z::11.660459518432617     color::0.35,0.0,0.0

d      URL::www.in.gr     coor_x::1.4531645774841309     coor_y::2.5  coor_z::11.660459518432617     color::0.35,0.0,0.0

e      URL::www.hotmail.com     coor_x::1.110593318939209      coor_y::2.5  coor_z::11.660459518432617     color::0.35,0.0,0.0

f      URL::www.yahoo.com       coor_x::2.9328434467315674     coor_y::3.2707982063293457     coor_z::11.660459518432617     color::0.35,0.0,0.0

g      URL::http://www.touchgraph.com/TGGoogleBrowser.php?start=g   coor_x::1.9439083337783813     coor_y::2.5  coor_z::11.660459518432617     color::0.35,0.0,0.0

h      URL::http://www.touchgraph.com/TGGoogleBrowser.php?start=h   coor_x::2.698544502258301      coor_y::2.5  coor_z::11.660459518432617     color::0.35,0.0,0.0

i      URL::http://www.touchgraph.com/TGGoogleBrowser.php?start=i   coor_x::2.389718532562256      coor_y::2.5  coor_z::11.660459518432617     color::0.35,0.0,0.0

end_of_layer_inputs

layer::chemicals   width::14.0  coor_x::0.0  coor_y::0.0  coor_z::7.440306663513184      angle_x::0.0       angle_y::0.0       angle_z::0.0       color::0.0,0.3,0.0      

a      URL::www.SKYPE.com       coor_x::3.0  coor_y::3.0  coor_z::3.8451543317565893     color::0.0,0.3,0.0

b      URL::www.java.org  coor_x::0.0  coor_y::3.0  coor_z::3.8451553317565867     color::0.0,0.3,0.0

c      URL::www.uoa.gr    coor_x::-3.0       coor_y::3.0  coor_z::3.8451563317565842     color::0.0,0.3,0.0

end_of_layer_inputs

layer::diseases    width::14.0  coor_x::0.0  coor_y::0.0  coor_z::-7.940305709838867     angle_x::0.0       angle_y::0.0       angle_z::0.0       color::0.49,0.34,0.0    

a      URL::www.pubmed.org      coor_x::0.0  coor_y::0.0  coor_z::-3.845151854919436     color::0.49,0.34,0.0

end_of_layer_inputs

layer::proteins    width::15.0  coor_x::0.0  coor_y::0.0  coor_z::-23.320919036865234    angle_x::0.0       angle_y::0.0       angle_z::0.0       color::0.34,0.0,0.34    

a      URL::www.ebi.ac.uk/      coor_x::4.0  coor_y::4.0  coor_z::-11.53545851843262     color::0.34,0.0,0.34

b      URL::www.leeds.ac.uk/    coor_x::0.0  coor_y::4.0  coor_z::-11.535457518432622    color::0.34,0.0,0.34

p30291       URL::http://www.touchgraph.com/TGGoogleBrowser.php?start=p30291    coor_x::-4.0       coor_y::4.0  coor_z::-11.535456518432625    color::0.34,0.0,0.34

go:aaa       URL::http://www.touchgraph.com/TGGoogleBrowser.php?start=go:aaa    coor_x::4.0  coor_y::0.0  coor_z::-11.535455518432627    color::0.34,0.0,0.34

end_of_layer_inputs

start_connections

a::pathways  b::pathways  5.099999904632568  VISIBLE::false

a::pathways  c::pathways  5.199999809265137

a::pathways  d::pathways  5.099999904632568

a::pathways  e::pathways  1.2000000476837158

a::pathways  f::pathways  1.2999999523162842

a::pathways  i::pathways  1.2999999523162842

b::pathways  c::pathways  5.199999809265137

b::pathways  d::pathways  1.100000023841858

b::pathways  e::pathways  1.2000000476837158

b::pathways  f::pathways  1.2999999523162842

c::pathways  f::pathways  1.2000000476837158

c::pathways  g::pathways  1.2999999523162842

c::pathways  h::pathways  1.2999999523162842

c::pathways  i::pathways  1.2999999523162842

d::pathways  e::pathways  6.099999904632568

d::pathways  f::pathways  6.199999809265137

d::pathways  g::pathways  1.3200000524520874

d::pathways  h::pathways  1.340000033378601

d::pathways  i::pathways  1.350000023841858

e::pathways  f::pathways  6.300000190734863

e::pathways  g::pathways  1.340000033378601

f::pathways  g::pathways  7.340000152587891

f::pathways  h::pathways  7.329999923706055

f::pathways  i::pathways  7.199999809265137

g::pathways  h::pathways  7.199999809265137

g::pathways  i::pathways  7.099999904632568

h::pathways  i::pathways  7.199999809265137

b::pathways  a::chemicals       1.399999976158142

c::pathways  a::chemicals       1.5

d::pathways  a::chemicals       1.600000023841858

e::pathways  a::chemicals       1.7000000476837158

f::pathways  a::chemicals       1.7999999523162842

c::chemicals       a::diseases  5.099999904632568

b::chemicals       a::diseases  1.899999976158142

a::diseases  a::proteins  2.0999999046325684

a::diseases  b::proteins  2.200000047683716

a::diseases  p30291::proteins   2.299999952316284

a::pathways  a::diseases  5.099999904632568

go:aaa::proteins   a::diseases  5.099999904632568

end_connections

 
 
European Molecular Biology Laboratory