Gaggle Microformat Reference

The Gaggle microformat allows embedding Gaggle data types in an HTML document. The Firegoose toolbar will detect data elements encoded in this format and make them available for broadcast to other Gaggle software or websites.

Use view source to examine the markup.

Microformats for Gaggle data types

This document contains examples of the Gaggle microformat for the following Gaggle data types:

Data TypeNameNotes
Name list gaggle-namelist An HTML list of identifiers.
Name list gaggle-namelist-tsv A tab separated list of identifiers.
Name list gaggle-namelist-tag A list constructed from all elements tagged with a particular CSS selector.
Map gaggle-map key/value pairs. Soon to be replaced.
Network gaggle-network An interaction network.
Data matrix gaggle-matrix A 2D grid of floating-point numbers with row and column labels encoded as an HTML table.
Data matrix gaggle-matrix-tsv A data matrix encoded as tab-separated values to reduce bloat.
Cluster gaggle-cluster A bicluster - a list of genes and conditions.

About Gaggle Microformats

Microformats are an easy way of allowing software tools to interpret the information presented in a web page. They are most useful for small chunks of data which can be presented to the user in a browser and, possibly, acted on by automated tools. Gaggle microformats are a literal translation of the Gaggle data types into microformats. It's probably impractical to embed large networks or data matrices in web pages. We're working on ways to indirectly reference large structures similar to the way graphics are referenced from <img> tags in HTML.

Name list:

name=Halo Genes
species=Halobacterium sp. NRC-1
(optional)size=11

  1. VNG0160G
  2. VNG0249G
  3. VNG0401G
  4. VNG0465G
  5. VNG0700G
  6. VNG0702H
  7. VNG1187G
  8. VNG1564H
  9. VNG1946G
  10. VNG2378G
  11. VNG2581H

Name list TSV:

name=Halo Genes (tsv)
species=Halobacterium sp. NRC-1
(optional)size=11

VNG0160G VNG0249G VNG0401G VNG0465G VNG0700G VNG0702H VNG1187G VNG1564H VNG1946G VNG2378G VNG2581H

Name list tagged:

The “tagged” list format can be used to embed a list in one column of a table, in a paragraph, or dispersed throughout the document. Note that a single HTML element can have multiple CSS selectors. This could be used to create overlapping lists or to style individual list items independently from their list membership.

name=Halo Genes (tag)
species=Halobacterium sp. NRC-1
(optional)size=9
CSS selector=names_test

boa1VNG0160G
fbrVNG0249G
epf2VNG0401G
nosF2VNG0465G
yvgXVNG0700G
VNG0702H
nirKVNG1187G

Let's not forget the genes in this paragraph - VNG2378G and VNG2581H!

Genes(16)

Halobacterium sp. NRC-1

genes

Map (key/value pairs):

Map is being replaced, so this structure is obsolete.

name=Annotations

species=Halobacterium sp. NRC-1

(optional)size=11

VNG0160G
Bacterio-opsin activator-like protein, Contains in N-C order PAS/PAC-GAF-HTH domains
VNG0249G
Copper binding proteins/plastocyanin/azurin
VNG0401G
mRNA 3'-end processing factor homolog
VNG0465G
ABC transporter, ATP-binding protein
VNG0700G
Copper (Cu) transporting P1-type ATPase
VNG0702H
heavy metal transport protein, A conserved 30-residue domain, Heavy-Metal-Associated (HMA), has been found in a number of these heavy metal transport or detoxification proteins. The domain contains two conserved cysteines that are probably involved in metal binding.
VNG1187G
putative Cu-containing nitrite reductase.
VNG1564H
VNG1946G
Formyltetrahydrofolate deformylase
VNG2378G
Copper transport ATP-binding protein
VNG2581H
heavy metal transport protein, A conserved 30-residue domain, Heavy-Metal-Associated (HMA), has been found in a number of such heavy metal transport or detoxification proteins. The domain contains two conserved cysteines probably involved in metal binding.

Interaction network

A graph with attributes assigned to nodes and edges, suitable for viewing in Cytoscape. Examples include protein-protein interaction networks and regulatory influence networks. In future versions, it will be possible to embed an indirect reference, rather than embedding a large network directly in a web page.

name=Protein Interactions

species=Halobacterium sp. NRC-1

(optional)size=5

Interactions

VNG2135Gembl stringVNG2138G
VNG2135Gembl stringVNG2139G
VNG2138Gembl stringVNG2139G
VNG0160G
VNG0249G

Node Attributes

VNG2135Gcommon nameatpD
VNG2139Gcommon nameatpA
VNG2138Gcommon nameatpB
VNG0160Gcommon nameboa1
VNG0249Gcommon namefbr

Edge Attributes

VNG2135G (embl string) VNG2138Gcombined association score0.991
VNG2135G (embl string) VNG2139Gcombined association score0.999
VNG2138G (embl string) VNG2139Gcombined association score0.999

Data Matrix

Embedding large matrices in a web page is of questionable value, but it is possible. A way to indirectly reference large data structures is planned for future versions of Firegoose.

name=Expression

description=copper time series data matrix

species=Halobacterium sp. NRC-1

(optional)size=11x9

GenesCu_-1_vs_NRC-1e.sigCu_000_vs_NRC-1e.sigCu_005_vs_NRC-1e.sigCu_010_vs_NRC-1e.sigCu_020_vs_NRC-1e.sigCu_040_vs_NRC-1e.sigCu_080_vs_NRC-1e.sigCu_160_vs_NRC-1e.sigCu_320_vs_NRC-1e.sig
VNG0160G-0.108-0.019-0.044-0.026-0.041-0.0320.013-0.161-0.111
VNG0249G0.230.2740.2520.1580.0090-0.1970.1220.2470.241
VNG0401G0.0850.0770.0580.0590.0460.040.0240.0630.069
VNG0465G0.0170.055-0.039-0.036-0.044-0.00300.0010-0.061-0.045
VNG0700G-0.079-0.0150.2150.5030.6720.6040.5680.2710.181
VNG0702H0.1110.1130.1250.2670.3680.3650.2190.10.117
VNG1187G-0.245-0.228-0.223-0.181-0.161-0.309-0.269-0.345-0.257
VNG1564H0.0280.0680.0910.0290.0530.0930.1070.080.074
VNG1946G0.0580.0240.0150.034-0.021-0.0030-0.0030-0.058-0.052
VNG2378G-0.0040-0.00700.041-0.00500.0270.0520.0230.0460.055
VNG2581H0.0710.10.3030.3240.4160.3790.3160.150.139

Cluster

Actually, a bicluster - a set of genes that are coregulated under a set of conditions.

clusterName=Sample Bicluster

description=a fake bicluster

species=Halobacterium sp. NRC-1

(optional)size=7x3

  1. VNG0160G
  2. VNG0249G
  3. VNG0401G
  4. VNG0465G
  5. VNG0700G
  6. VNG0702H
  7. VNG1187G
  1. Cu_010_vs_NRC-1e.sig
  2. Cu_020_vs_NRC-1e.sig
  3. Cu_040_vs_NRC-1e.sig

validate