bbabbd5d2566d47d923d51dbe350634783455999
mspeir
Sun Oct 26 12:14:52 2025 -0700
change soe to gi, refs #35031
diff --git src/hg/htdocs/goldenPath/help/hgGeneGraph.html src/hg/htdocs/goldenPath/help/hgGeneGraph.html
index 3ddaf7d54c9..781e4904e96 100755
--- src/hg/htdocs/goldenPath/help/hgGeneGraph.html
+++ src/hg/htdocs/goldenPath/help/hgGeneGraph.html
@@ -205,52 +205,52 @@
iRefIndex 13 which includes
BIND,
BioGRID,
CORUM,
DIP,
HPRD,
InnateDB,
IntAct,
MatrixDB,
MINT,
MPact,
MPIDB and
MPPI
Androgen Responsive
Gene Database. This database is not available anymore on the internet, but we kept
- a copy.
+ a copy.
String 9.1
Negatome 2.0
Corum Protein Complexes
Gene Ontology Protein Complexes
Pathways
The quantitative contribution of each database in terms of number of gene-pairs is available
here.
@@ -271,31 +271,31 @@
Data Access
The raw data for these graphs can be accessed in multiple ways. They can be explored interactively
using the Table Browser, by selecting "group" -
"All Tables"
and "database" - "hgFixed". Under "table", select
"hgFixed.ggLink". You can then start to explore the
relationships between the database tables using the "data format description" button or
download tables with "get output". All database tables related to this viewer start with
the prefix "gg".
The database tables can also be accessed programmatically through our
public MariaDB server or downloaded from our
- downloads server for local
+ downloads server for local
processing. The database tables are:
- ggLink - one row per gene/gene interaction. The field "minResCount" is
the minimum number of interactions obtained from the same supporting article.
E.g. if it is 10, then out of all supporting articles, there is one with 10 interactions
curated from it and maybe others with more interactions. A cutoff of 50 should remove
high-throughput data from the table. Note that while most databases are in the format source
-> target, in this table, the target comes first and the source second. Gene names are
separated by the "|"-symbol.
- ggLinkEvent - connections between a ggLink and one of the ggEvent tables.
The prefix of the eventId indicates the table: ppi/pwy links to ggEventDb, msr links
to ggEventText.
- ggEventDb - information about gene/gene interactions imported from protein
interaction or pathway databases. The structure is modeled after the NCI PID interactions
data schema and distinguishes genes, complexes and compounds on each side of the reaction,
@@ -303,31 +303,31 @@
are part of the table but not shown in our user interface.
- ggEventText - information about gene/gene interactions obtained from
text mining.
- ggDocEvent - connections between documents and events.
- ggDoc - information about documents referenced from ggEventText and ggDocEvent.
- ggGeneClass - the HPRD/Panther class, one for each gene symbol.
- ggGeneName - the HGNC name, one for each gene symbol.
For more details about the tables and their fields, use the Table Browser's
"describe schema" button.
The annotations (GNF2 average expression, DrugBank, etc.) for genes are accessed as text files
for performance reasons and can be downloaded from our
- downloads server.
+ downloads server.
Credits
- The text-mined data for the gene interactions and pathways were generated by Chris Quirk and
Hoifung Poon as part of Microsoft Research Project Hanover.
- Pathway data was provided by the databases listed under methods.
- Thanks to Ian Donaldson for IRefIndex, the biggest and free collection of protein interaction databases.
- Arjun Rao (UCSC) provided the ArgDB converter.
- Thanks to Dexter Pratt for help with OpenBEL and to Charles Tepley Hoyt for the
pybel converter.
- Thanks to Alexander Pico for help with the WikiPathways data format GPML
- The short gene descriptions are a merge of the