Data storage and AmiGO 2 Working Group Meetings

Data storage and AmiGO 2 call 1-30-15

• Who: PJ, CM, Seth, EZ, LC, JP, JE
• Discussion of the planned transition to the AmiGO 2.0 platform
• JE is working on installing SolR database - View details and progress reports here: AmiGO2_install

Data Storage and AmiGO2 call 2-18-15

• Who: JE, JP, EZ
• Link to video recording: Media:Data_Storage_2-18-15.mp4
• Link to audio recording: File:Data Storage Meeting audio only 2-18-15.m4a

• Further discussion of AmiGO2 progress and overview of AmiGO2 interface

Planteome Interface meeting 3-2-15

Who: EZ, LC, JE, PJ ...??

• Link to video recording: File:Planteome Interface mtg video 3-2-15.mp4
• Link to audio recording: File:Planteome Interface mtg audio 3-2-15.m4a

• EZ: First thing: focus of the project, speed up queries, data visualization, data organization
• User Interface: it would be good to see how the users operate and what kinds of questions they would ask.
• Amigo 2, could build enhanced interface so users could inspect their data and build queries.
• what functionalities are needed?
• Questions:
  • How will the users access the interface?
  • How will they use the interface?

Involvement of other organisms? e.g. viruses, animals, etc

• Could the tools be expanded to other organisms
• Crops are interacting with the environment, other organisms

AmiGO2 introduction

• show filtered image
• Cytoscape Sif file, ontology network
• bring in other ontologies, Rice Xanthomanas example
• ontology formats

Data storage and AmiGO2 Working Group Meeting 4-16-15

Who: EZ, BQ, PJ, JP, LC, JE

• Link to video recording: File:Data storage and AmiGO2 video 4-16 15.mp4
• Link to audio recording: File:Data storage and AmiGO2 audio 4-16 15.m4a

• Introductions
• Storing code developed on Planteome project on Github
• posting notes on wiki
• data visualization aspect within AmiGO2- work with JE on
• Data annotation- wikipedia style?
• different levels of access
• To do: Send link to Eugene and Botong- circulate the developer position ad

Relevant links:

• https://github.com/geneontology/amigo
• Demo: http://amigo.geneontology.org/
• http://amigo2.berkeleybop.org/ - dev server

Data storage and AmiGO2 Working Group meeting 5-1-15

Who: PJ, BQ, EZ, CM, JE

• Link to video: File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4
• Link to audio: File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a

Demo of GO enrichment tool

• At the GO website (www.geneontology.org)
• See how it works there compared to the one at AGRIGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php). See if your NIH proposal work with Yanmin Di overlaps and can be adopted.

• Set of genes you can get a list of Arabidopsis thaliana genes from the attached file. (email)
• Gene pages at Gramene e.g. http://archive.gramene.org/db/genes/search_gene?acc=GR:0101175 or elsewhere
• Start thinking about building a gene database, with different access levels for admins and curators, limited in what fields are allowed to be edited by what level.

This is for building the community gene annotation tools. The annotated data from this database can be synced with the AmiGOdb version that Justin Elser and Chris are working on.

I hope this will give Bo, enough width to work until the AMIGO build and datasets mature.

BinGO http://bioinformatics.oxfordjournals.org/content/21/16/3448.full AgriGO http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/

Data storage and AmiGO2 Working Group Meeting 5-15-15

Who: PJ, EZ, BQ, JE, CM

• Continue to show how the enrichment analysis tools work(agriGO).
• Discuss about the language and character problem on the page.
• Agreed to start with design the requirement specification.
• Share the old database scheme with EZ and BQ.
• Show the Annotation database to EZ and BQ (unfinished, need to be continued).

EZ and BQ will start with analyzing the old database scheme and try to study the enrichment analysis algorithms, the first goal of the group is to show the search result through tables. The next step will be visualize it with Graph.

Data storage and visualization Working Group Meeting 5-27-15

Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)

Link to recordings (in 2 parts):

• Audio P.1: File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a
• Video P.1: File:Planteome Data Vis Mtg p1 5-27-15-video.mp4
• Audio P.2: File:Data Visualization 5-27-15 audio.m4a
• Video P.2: File:Data Visualization 5-27-15 part 2.mp4

Intro to Planteome for to new students

• Explanation of ontologies
• Overview of older AmiGO browser
• Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology [1]
  • Used gene set from planteome.cgrb to demonstrate AgriGO usage

Data storage and visualization Working Group Meeting 6-3-15

Who: EZ, PJ, LC, JP, Christian and Marquis (REU students) Location: Kelley 2057 (KEC)

Link to recordings (in 3 parts):

• Video P.1: File:Data Store meeting p1 6-3-15 video.mp4
• Video P.2: File:Data Store meeting p2 6-3-15 video.mp4
• Video P.3: File:Data Store Meeting p3 6-3-15 video.mp4

Database discussion

• Discussion of the legacy gene database schema for the Plant Ontology - 36 tables

Example fields in gene table

Data storage and visualization Working Group Meeting 8-26-15

Who: EZ, PJ, JE, Jaden, Botong, CM Location: Kelley 2057 (KEC)

Link to recording

field name	comment
gene symbol	?
gene name	?
synonyms	one to many
ontology ID	Ontology term name