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.

Microformats for Gaggle data types

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

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:

Data Type	Name	Notes
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.

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

VNG0160G
VNG0249G
VNG0401G
VNG0465G
VNG0700G
VNG0702H
VNG1187G
VNG1564H
VNG1946G
VNG2378G
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

Genes(16)

Halobacterium sp. NRC-1

genes

VNG0524G
VNG0527C
VNG0629G
VNG0657G
VNG0662G
VNG0665G
VNG0717H
VNG1114G
VNG1123G
VNG1771C
VNG1866G
VNG2043G
VNG6294G
VNG6315G
VNG6316G
VNG6317G

Map (key/value pairs):

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

VNG2135G	embl string	VNG2138G
VNG2135G	embl string	VNG2139G
VNG2138G	embl string	VNG2139G
VNG0160G
VNG0249G

Node Attributes

VNG2135G	common name	atpD
VNG2139G	common name	atpA
VNG2138G	common name	atpB
VNG0160G	common name	boa1
VNG0249G	common name	fbr

Edge Attributes

VNG2135G (embl string) VNG2138G	combined association score	0.991
VNG2135G (embl string) VNG2139G	combined association score	0.999
VNG2138G (embl string) VNG2139G	combined association score	0.999

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

Genes	Cu_-1_vs_NRC-1e.sig	Cu_000_vs_NRC-1e.sig	Cu_005_vs_NRC-1e.sig	Cu_010_vs_NRC-1e.sig	Cu_020_vs_NRC-1e.sig	Cu_040_vs_NRC-1e.sig	Cu_080_vs_NRC-1e.sig	Cu_160_vs_NRC-1e.sig	Cu_320_vs_NRC-1e.sig
VNG0160G	-0.108	-0.019	-0.044	-0.026	-0.041	-0.032	0.013	-0.161	-0.111
VNG0249G	0.23	0.274	0.252	0.158	0.0090	-0.197	0.122	0.247	0.241
VNG0401G	0.085	0.077	0.058	0.059	0.046	0.04	0.024	0.063	0.069
VNG0465G	0.017	0.055	-0.039	-0.036	-0.044	-0.0030	0.0010	-0.061	-0.045
VNG0700G	-0.079	-0.015	0.215	0.503	0.672	0.604	0.568	0.271	0.181
VNG0702H	0.111	0.113	0.125	0.267	0.368	0.365	0.219	0.1	0.117
VNG1187G	-0.245	-0.228	-0.223	-0.181	-0.161	-0.309	-0.269	-0.345	-0.257
VNG1564H	0.028	0.068	0.091	0.029	0.053	0.093	0.107	0.08	0.074
VNG1946G	0.058	0.024	0.015	0.034	-0.021	-0.0030	-0.0030	-0.058	-0.052
VNG2378G	-0.0040	-0.0070	0.041	-0.0050	0.027	0.052	0.023	0.046	0.055
VNG2581H	0.071	0.1	0.303	0.324	0.416	0.379	0.316	0.15	0.139

name=Expression (tsv)

description=copper time series data matrix (tsv)

species=Halobacterium sp. NRC-1

(optional)size=11x9

GENE Cu_-1_vs_NRC-1e.sig Cu_000_vs_NRC-1e.sig Cu_005_vs_NRC-1e.sig Cu_010_vs_NRC-1e.sig Cu_020_vs_NRC-1e.sig Cu_040_vs_NRC-1e.sig Cu_080_vs_NRC-1e.sig Cu_160_vs_NRC-1e.sig Cu_320_vs_NRC-1e.sig VNG0160G -0.108 -0.019 -0.044 -0.026 -0.041 -0.032 0.013 -0.161 -0.111 VNG0249G 0.23 0.274 0.252 0.158 0.0090 -0.197 0.122 0.247 0.241 VNG0401G 0.085 0.077 0.058 0.059 0.046 0.04 0.024 0.063 0.069 VNG0465G 0.017 0.055 -0.039 -0.036 -0.044 -0.0030 0.0010 -0.061 -0.045 VNG0700G -0.079 -0.015 0.215 0.503 0.672 0.604 0.568 0.271 0.181 VNG0702H 0.111 0.113 0.125 0.267 0.368 0.365 0.219 0.1 0.117 VNG1187G -0.245 -0.228 -0.223 -0.181 -0.161 -0.309 -0.269 -0.345 -0.257 VNG1564H 0.028 0.068 0.091 0.029 0.053 0.093 0.107 0.08 0.074 VNG1946G 0.058 0.024 0.015 0.034 -0.021 -0.0030 -0.0030 -0.058 -0.052 VNG2378G -0.0040 -0.0070 0.041 -0.0050 0.027 0.052 0.023 0.046 0.055 VNG2581H 0.071 0.1 0.303 0.324 0.416 0.379 0.316 0.15 0.139

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

VNG0160G
VNG0249G
VNG0401G
VNG0465G
VNG0700G
VNG0702H
VNG1187G

Cu_010_vs_NRC-1e.sig
Cu_020_vs_NRC-1e.sig
Cu_040_vs_NRC-1e.sig