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Review MassBank markup and add to LiveDeploys #198

Closed AlasdairGray closed 3 years ago

AlasdairGray commented 6 years ago

MassBank have been adding DataCatalog and Dataset markup. This should be reviewed and then added to the live deploys list.

kcmcleod commented 6 years ago

No schema of any kind currently visible in their pages. Alasdair has already emailed to ask for links to pages with markup

https://search.google.com/structured-data/testing-tool#url=https%3A%2F%2Fmassbank.eu%2FMassBank%2F

Treutler commented 6 years ago

The schema is not live in the official MassBank.eu. We have a testing instance at the IPB: https://msbi.ipb-halle.de/MassBank/

Here we implemented the Dataset markup for records, e.g. here. In addition, we implemented the DataCatalog markup in the record index: here.

We would also test some chemical markup when possible. It would be great if you could have an eye on our present stuff! Best regards, Hendrik

egonw commented 6 years ago

Some initial feedback on the Dataset markup:

I see the embedded RDFa, but it seems that Google does not pick that up properly...

AlasdairGray commented 6 years ago

I don't think that this should be marked up as a Dataset. I think that this is one record within a Dataset and the record is about a Chemical Substance.

I see the embedded RDFa, but it seems that Google does not pick that up properly...

Google was certainly picking up some of the RDFa. However, JSON-LD is the preferred form of markup both for Google and for Bioschemas.

egonw commented 6 years ago

@Treutler, does the website software allow for adding content to the HTML <head>? If so, I would recommend using JSON-LD instead of RDFa. See:

These are examples of the JSON-LD you can add to your page. See also the "Adding the script to your website" section on this page: https://yoast.com/json-ld/

egonw commented 6 years ago

@AlasdairGray, the link I posted was given in one of the earlier comments of where Dataset was implemented.

AlasdairGray commented 4 years ago

Thanks for the contribution of markup within MassBank. As discussed in PR 274 there are some refinements that should be made.

You should ensure that there are different identifiers used for the DataRecord (currently Dataset) and the MolecularEntity.

Once you've made these refinements, we'll be able to add you to the DataRecord, Dataset, and DataCatalog list of live deploys.

AlasdairGray commented 3 years ago

This is related to #475 and the markup should reflect the outcome of that discussion. At the moment, the markup tries to distinguish two resources, but uses the same identifier for them.


[
{
"identifier": "LQB00001",
"url": "https://massbank.eu/MassBank/RecordDisplay?id=LQB00001",
"name": "Cer[AP] t34:0",
"alternateName": "Cer[AP] t34:0",
"inchikey": "RHIXBFQKTNYVCX-UHFFFAOYSA-N",
"description": "This MassBank record with Accession LQB00001 contains the MS2 mass spectrum of 'Cer[AP] t34:0'.",
"molecularFormula": "C34H69NO5",
"monoisotopicMolecularWeight": "571.928",
"inChI": "InChI=1S/C34H69NO5/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-31(37)33(39)30(29-36)35-34(40)32(38)28-26-24-22-20-18-16-14-12-10-8-6-4-2/h30-33,36-39H,3-29H2,1-2H3,(H,35,40)",
"smiles": "CCCCCCCCCCCCCCC(O)C(O)C(CO)NC(=O)C(O)CCCCCCCCCCCCCC",
"@context": "http://schema.org",
"@type": "MolecularEntity"
},
{
"identifier": "LQB00001",
"url": "https://massbank.eu/MassBank/RecordDisplay?id=LQB00001",
"headline": "Cer[AP] t34:0; LC-ESI-QTOF; MS2",
"name": "Cer[AP] t34:0",
"description": "This MassBank record with Accession LQB00001 contains the MS2 mass spectrum of 'Cer[AP] t34:0'.",
"datePublished": "2016-10-03",
"license": "https://creativecommons.org/licenses",
"citation": "null",
"comment": "Found in mouse small intestine; TwoDicalId=238; MgfFile=160907_Small_Intestine_normal_Neg_01_never; MgfId=1081",
"alternateName": "Cer[AP] t34:0",
"@context": "http://schema.org",
"@type": "Dataset"
}
]
meier-rene commented 3 years ago

We need more hand holding please. What are the negative consequences of the current markup? How could we improve the situation?

Adding @sneumann also...

sneumann commented 3 years ago

Can we also have hand-holding here to implement the todos in https://github.com/BioSchemas/specifications/issues/198#issuecomment-698927151 ? Best would be URLs of resources correctly implementing that for inspiration (e.g. LandingPage markup, schema:xxx properties etc. Alternatively Links to docs how to implement. Yours, Steffen

egonw commented 3 years ago

Part of LiveDeploys now:

image