Content Pages

[ktun95]

Terms:
I've annotated each link using the following terms below. I've provided explanations for what I mean by each term.

[Formatting Issues] Usually an issue with bullet or numbered lists
[Missing Page] No content at all. Directs to Not Found page.
[Missing Content] The page exists, but the intended content is not yet there.
[Broken Links] There are links present, but the content at the URL is missing/broken
[Missing Links] There seems to be text where links were intended to be, but there is none

Issues

/community/citation - Formatting Issues
/about - Missing Page
/explore/art - Missing image
/explore/gallery - Missing Content
/explore/teach - Broken Links

• All Experiments links are broken

/explore/links - Broken Links

Some of the Broken Links from /explore/links

Gene and Protein Analysis:
    - dictyExpress: Gene expression data visualization in Dictyostelium
    - The Eumycetozoan Project: Ecology, systematics and evolution of Myxomycetes, Dictyostelids and Protostelids 
    - NIH Model Organisms for Biomedical Research: Dictyostelium discoideum
    - TKE Connections Map (Science)
    - STKE summary (dictyBase)
    - Swiss-Prot: annotated Dictyostelium proteins
    - AmiGO: Web-based browser for The Gene Ontology
    - Apollo: A Java-based application for annotating genomic sequences
    - BRENDA: The Comprehensive Enzyme Information System
    - Chado: The GMOD database schema
    - InParanoid: Database of eukaryotic ortholog groups

Molecular Pathways:
    - ExPASy Biochemical Pathways: Digitized version of the Roche Applied Science "Biochemical Pathways" wall chart
    - Reactome: A knowledgebase of biological processes

Protein Family Information:
    - ChromDB: The Plant Chromatin Database
    - Cytochrome P450 Homepage
    - GPCRDB: Information system for G protein-coupled receptors (GPCRs)
    - Kinesins
    - The Protein Kinase Resource
    - Splicing Related Gene Database

[...I stopped checking after these, but I can complete this list if it would be helpful]

/research/techniques - Missing Links
/research/techniques/rnai-procedure - Missing Content
/research/techniques/* - Formatting Issues

• Various techniques pages linked in /research/techniques have formatting issues, usually relating to bulleted or numbered lists

/research/ontology - Formatting Issues, Broken Link

• EBI's ontology browser tool Link is broken

/research/codon - Missing Content
/research/nomenclature - Formatting Issues
/research/phenotype - Missing Content
/stockcenter/information/faq - Formatting Issues
/community/listserv - Missing Content?
/community/labs - Broken Links

[rjdodson]

/community/citation - Formatting Issues: Corrected!
/about - Missing Page: Skipping this for now, this is not mission critical and needs further thought and input
/explore/art - Missing image: Skipping for now, not sure how to add this image
/explore/gallery - Missing Content: Skippping for now, this will require users to submit images and videos

/explore/teach - Broken Links

All Experiments links are broken: Could not find any of the links, but sent an email to the responsible researcher, David Knecht, asking if the links are still available somewhere

I will continue from this point sometime later.

[ktun95]

Footer

/dictyaccess - Missing Page
/contact - Missing Page

Main

New Stock Center Items

Links under New Stock Center Items are still placeholders and only route to /stockcenter

[rjdodson]

/explore/teach - Broken LinksAll Experiments links are broken: David Knecht has emailed back. He is retired and there is no url available, but he will email pdfs of all the experiments so that we can provide an internal link to the experiments

/explore/links - Broken Links

CBS Prediction Servers is also broken with message: The servers are being moved to a different physical location. We are taking this opportunity to restructure our server park.
The discontinued web site www.cbs.dtu.dk will be retired. We will need to decide which of these services to include and provide specific links to each

dictyExpress: Gene expression data visualization in Dictyostelium: restored link; linked to Shaulsky and Kuspa's website

DictyOGlyc 1.1 Server: replaced old with new link (https://services.healthtech.dtu.dk/services/DictyOGlyc-1.1/)

• The Eumycetozoan Project: Not found
• NIH Model Organisms for Biomedical Research: Dictyostelium discoideum: Not Found
• • STKE summary (dictyBase) Not found
• • Swiss-Prot: annotated Dictyostelium proteins: Renamed, fixed link
• AmiGO: Web-based browser for The Gene Ontology: correct link restored
• Apollo: A Java-based application for annotating genomic sequences: correct link restored
• BRENDA: The Comprehensive Enzyme Information System: correct link restored
• • Chado: The GMOD database schema: link restored
• GBrowse: The Generic Genome Browser: link restored
• GMOD: link restored
• • InParanoid: Database of eukaryotic ortholog groups: link restored

[rjdodson]

Note to self: continue revising links beginning at http://dictybase.org/Dicty_Info/other_links.htm Bioinformatics Resources

[rjdodson]

All links in https://dictybase.dev/explore/links Bioinformatics Resource either verified or corrected
Molecular Pathways:
ExPasy Biochemical Pathways: Not found
Protein Family Information
Repaired links for most
Kinesins: Not found
Removed Splicing related gene database: http://pkr.sdsc.edu/html/index.shtml, not found and link is misleading

Continue with links for Other model organism databases

[rjdodson]

List of deleted links:

dictybase.dev/explore/links

The Eumycetozoan Project: Ecology, systematics and evolution of Myxomycetes, Dictyostelids and Protostelids

NIH Model Organisms for Biomedical Research: Dictyostelium discoideum

STKE Connections Map (Science) - STKE summary (dictyBase)

ExPASy Biochemical Pathways: Digitized version of the Roche Applied Science "Biochemical Pathways" wall chart

AgBase: Resource for functional analysis of agricultural plant and animal gene products

Entamoeba histolytica Genome Project

J. Craig Venter Institute (formerly TIGR) Genome Projects

[rjdodson]

List of deleted links:

Nature's genome gateway: A comprehensive web resource devoted to genomics

Infotrieve

[rjdodson]

deleted links:

Research/techniques:

Making double mutants by diploid genetics (contributed by Jason King and Robert Insall) (this was a duplicate with parasexual genetics

[rjdodson]

/research/techniques - Added Missing Links!
/research/techniques/rnai-procedure - Added Missing Content!

/research/techniques/* - Formatting Issues (Some formatting issues remain)

Various techniques pages linked in /research/techniques have formatting issues, usually relating to bulleted or numbered lists

/research/ontology - Formatting Issues, Broken Link

EBI's ontology browser tool Link is broken Fixed!!

[rjdodson]

/research/codon - Missing Content At dictyBase, this links to an external website. Easiest fix would be to modify the link from the home page, but I am not sure how to do that
/research/nomenclature - Formatting Issues Fixed