HELP - Verifying Wiki Content about pheknowlator HOT 14 CLOSED

KG Construction

• "The OWLTools command line tool is used to download all ontologies. " - dead link
• "This tool is useful because it ensures that all ontologies imported by the ontology being downloaded are also downloaded and merged together." -- Would it be accurate saying something like this instead to be more clear? "This tool is useful because it ensures that all secondary ontologies imported by the primary ontology are also downloaded and merged together.
• "These steps are important and may require consulting with an expert." - what kinda expert?
• You bounce between using "EXAMPLE" and "Example" (underlined). Consider being consistent.
• Wiki Page: Dependencies
• The beginning of the 'Dependencies' page as does the previous page says 'preparation of three documents' and then lists 8 things? What are the three documents?
• "Edge Type: An edge label (node1-node2) should match Data Sources in the ontology, class edge, and non-class edge input files." - class edge link is broken
• "Source labels: Three ; separated items (e.g.:;GO_;GO_): character to split existing labels (e.g. : in GO:1283834) and label for subject and object nodes. If the existing label is correct, type ;;." - The first sentence isn't a complete sentence. I don't understand the '): character to split existing labels" segment. Should there be a comma and a space in between the parenthesis and colon '), :'?
• "https://reactome.org/content/detail/" - broken link
• [Construction Approach](Construction Approach) - this links back to the KG Construction page, making a loop. I'm confused.
• What's a "UUID"?
• "An example list can be found here." - dead link

@jwyrwa - very helpful, thank you!! I have updated everything to reflect what you commented on. The following two points you made:

• [Construction Approach](Construction Approach) - this links back to the KG Construction page, making a loop. I'm confused.
• "https://reactome.org/content/detail/" - broken link

Are actually OK and functioning fine.

For the point about the source labels, I tried to improve the language and changed it to the following:

`Source labels: Three ;-separated items (e.g.:;GO_;GO_). The first item (i.e. ':') is a character that is used to split existing labels (e.g. : in GO:1283834), such that all characters that occur before that label are replaced by the content provided after the first and second ';' (i.e. 'GO_' and 'GO_'). If the existing label is correct, type ;;.

Does that make more sense?

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Yup.

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Reasoner Evaluation

• I made a few grammar changes.
• I love the name 'Chainsaw' for a reasoner.
• I added my degree so I'm not just some random user.

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v2 Data Sources

• I'm not even going to pretend that I understood even 1% of this page.

• "ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt" - 404 error

• "compath_cannonical_pathway_mappings.txt" - mismatch between display name and file name. Not sure which is correct.

• "Protein Ontology" - o.0 is the 'ontology download' page supposed to look like that?

• "Notes: The ontology was filtered to only include human proteins using a list of of human proteins by generating a new human-only version of the ontology. Details on how this version of the ontology was generated can be found here, under the Protein Ontology section." - would it still be accurate to condense this to "A partial, human-only version of this ontology was used. Details on how this version of the ontology was generated can be found here, under the Protein Ontology section." ?

• "Merged Gene, RNA, Protein Map: Merged_gene_rna_protein_identifiers.pkl" is this meant to be indented?

• "Homepage: BioPortal" - is this the link that you intended? I was expecting this.

• Homo_sapiens.GRCh38.98.uniprot.tsv.gz - ERR_FTP_FAILED

• "Usage: Utilized to create edges between non-coding rna-cell and non-coding rna-anatomy edges." - edges can be made between edges?

• "Zooma was utilized to automatically the 153 unique tissues and cell types from Human Protein Atlas for all human protein-coding genes in the Human Proteome to the Cell Ontology, Cell Line Ontology, and the Uber-Anatomy Ontology." - Zooma did what automatically?

• "Parsing NCBI Gene data to obtain mappings between NCBI Gene identifiers](#ncbi-gene)," - is this supposed to be a link?

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Home

• 'Data for this release can be downloaded here' - This link doesn't scroll like I think you were expecting. It looks like the URL might need to be this
• 'We presented this work (poster) at the 15th Annual Rocky Mountain Bioinformatics Conference held December 6-8th in Snowmass, Colorado.' - Why is the poster file titled 'Rocky2017' but the link to the conference is for 2018?

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Home

• 'Data for this release can be downloaded here' - This link doesn't scroll like I think you were expecting. It looks like the URL might need to be this
• 'We presented this work (poster) at the 15th Annual Rocky Mountain Bioinformatics Conference held December 6-8th in Snowmass, Colorado.' - Why is the poster file titled 'Rocky2017' but the link to the conference is for 2018?

Good catch! I have updated both URLs.

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KG Construction

• "The OWLTools command line tool is used to download all ontologies. " - dead link

• "This tool is useful because it ensures that all ontologies imported by the ontology being downloaded are also downloaded and merged together." -- Would it be accurate saying something like this instead to be more clear? "This tool is useful because it ensures that all secondary ontologies imported by the primary ontology are also downloaded and merged together.

• "These steps are important and may require consulting with an expert." - what kinda expert?

• You bounce between using "EXAMPLE" and "Example" (underlined). Consider being consistent.

• Wiki Page: Dependencies

• The beginning of the 'Dependencies' page as does the previous page says 'preparation of three documents' and then lists 8 things? What are the three documents?

• "Edge Type: An edge label (node1-node2) should match Data Sources in the ontology, class edge, and non-class edge input files." - class edge link is broken

• "Source labels: Three ; separated items (e.g.:;GO_;GO_): character to split existing labels (e.g. : in GO:1283834) and label for subject and object nodes. If the existing label is correct, type ;;." - The first sentence isn't a complete sentence. I don't understand the '): character to split existing labels" segment. Should there be a comma and a space in between the parenthesis and colon '), :'?

• "https://reactome.org/content/detail/" - broken link

• [Construction Approach](Construction Approach) - this links back to the KG Construction page, making a loop. I'm confused.

• What's a "UUID"?

• "An example list can be found here." - dead link

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Should OWL always be all caps? 'owl' is used in some cases.

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Should OWL always be all caps? 'owl' is used in some cases.

It should be all caps. Are the lowercase uses in code blocks? If so, that's OK.

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OWL NETS 2.0

• I tried putting a dash in the title of the page, but it won't stick :(

• "A json file or dict() mapping an owl:Class to an instance of the owl:class (primarily used for PheKnowLator, for example:" - should both be 'Class' or 'class'? Is there a missing parenthesis?

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OWL NETS 2.0

• I tried putting a dash in the title of the page, but it won't stick :(

• If you are talking about the header at the very top of the WIki page, then yeah that's something we can't change. Thanks for trying though!

• "A json file or dict() mapping an owl:Class to an instance of the owl:class (primarily used for PheKnowLator, for example:" - should both be 'Class' or 'class'? Is there a missing parenthesis?

Ahh, this part actually needs to be removed to reflect the refactoring I did to simplify this method. I have updated that section now. Thanks for catching that!

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v2.0.0

• "Added Data_Preparation.ipynb Jupyter Notebook to aid in creation of mapping, filtering, and labeling datasets
  Added Ontology_Cleaning.ipynb Jupyter Notebook to aid in creation of mapping, filtering, and labeling datasets" - these both do the same thing? Could I just collapse it into "Added Data_Preparation.ipynb and Ontology_Cleaning.ipynb Jupyter Notebooks to aid in creation of mapping, filtering, and labeling datasets"

• Ontologies - all of the links are broken (404 error)

• "Relations and Inverse Relations ➞ INVERSE_RELATIONS.txt
  Relations and Labels ➞ RELATIONS_LABELS.txt" - 404 errors

• "STANDARD RELATIONS", "Edge Lists", "Node Metadata" - all of the links in this table take me to a 'Create new page'

• "Generated Output", "Generated Output" - are these (almost) exactly the same? All the same links in both sections are having the same issue I described above. Thoughts on condensing into one 'Generated Output' Section that has something like "Common Output" and then having "Unique to Subclass-Based Construction" and "Unique to Instance-Based Construction"? It'll cut down on redundancies and make it easier to maintain.

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v2.0.0

• "Added Data_Preparation.ipynb Jupyter Notebook to aid in creation of mapping, filtering, and labeling datasets
  Added Ontology_Cleaning.ipynb Jupyter Notebook to aid in creation of mapping, filtering, and labeling datasets" - these both do the same thing? Could I just collapse it into "Added Data_Preparation.ipynb and Ontology_Cleaning.ipynb Jupyter Notebooks to aid in creation of mapping, filtering, and labeling datasets"

Fixed, the text should not have been the same. Thanks for catching that!

• Ontologies - all of the links are broken (404 error)
  Fixed!

• "Relations and Inverse Relations ➞ INVERSE_RELATIONS.txt
  Relations and Labels ➞ RELATIONS_LABELS.txt" - 404 errors
  Fixed!

• "STANDARD RELATIONS", "Edge Lists", "Node Metadata" - all of the links in this table take me to a 'Create new page'
  Yes, sorry, these links will be down until results are finished.

• "Generated Output", "Generated Output" - are these (almost) exactly the same? All the same links in both sections are having the same issue I described above. Thoughts on condensing into one 'Generated Output' Section that has something like "Common Output" and then having "Unique to Subclass-Based Construction" and "Unique to Instance-Based Construction"? It'll cut down on redundancies and make it easier to maintain.
  Yes, sorry, these links will be down until results are finished. They will point to different things.

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Thank you so much @jwyrwa !! This was incredibly helpful I have made all suggested changes and will now close this issue!

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