Signposting and Webby FDOs

Stian Soiland-Reyes, The University of Manchester, UK

Motivation

How to find the way from persistent identifiers,

through a repository

to find data and metadata

A typical PID resolution

GET https://doi.org/10.abcd/j.mystery.14

HTTP/1.1 302 Found
Location: http://example.com/repo/item/14

Browsers follow redirection to the repository's landing page

GET http://example.com/repo/item/14

HTTP/1.1 200 OK
Content-Type: text/html

<html>
  <head> … </head>
  <body>
  …
  </body>
</html>

HTML for human readability and human navigation

A preview of the resource

Metadata (e.g. title, description) as text

Link to download (pdf, zip)

.. and many unrelated links

There may be multiple downloads, multiple metadata formats

Multiple metadata formats

{
  "@context": "http://schema.org",
  "id": "https://doi.org/10.5281/zenodo.10847062",
  "type": "https://schema.org/PresentationDigitalDocument",
  "author": [
    {
      "id": "https://orcid.org/0000-0001-9842-9718",
      "type": "Person",
      "affiliation": [
        {
          "id": "https://ror.org/027m9bs27",
          "type": "Organization",
          "name": "University of Manchester"
        },
        {
          "id": "https://ror.org/04dkp9463",
          "type": "Organization",
          "name": "University of Amsterdam"
        }
      ],
      "familyName": "Soiland-Reyes",
      "givenName": "Stian",
      "name": "Soiland-Reyes, Stian"
    },
    {
      "id": "https://orcid.org/0000-0002-0715-6126",
      "type": "Person",
      "familyName": "Van de Sompel",
      "givenName": "Herbert",
      "name": "Van de Sompel, Herbert"
    }
  ],
  "contentSize": "11.95 MB",
  "creator": [
    {
      "id": "https://orcid.org/0000-0001-9842-9718",
      "type": "Person",
      "affiliation": [
        {
          "id": "https://ror.org/027m9bs27",
          "type": "Organization",
          "name": "University of Manchester"
        },
        {
          "id": "https://ror.org/04dkp9463",
          "type": "Organization",
          "name": "University of Amsterdam"
        }
      ],
      "familyName": "Soiland-Reyes",
      "givenName": "Stian",
      "name": "Soiland-Reyes, Stian"
    },
    {
      "id": "https://orcid.org/0000-0002-0715-6126",
      "type": "Person",
      "familyName": "Van de Sompel",
      "givenName": "Herbert",
      "name": "Van de Sompel, Herbert"
    }
  ],
  "dateCreated": "2024-03-21T07:52:03.534671+00:00",
  "dateModified": "2024-07-06T20:35:20.427129+00:00",
  "datePublished": "2024-03-21",
  "description": "<p>Presented at FDO Summit 2024</p>",
  "identifier": "https://doi.org/10.5281/zenodo.10847062",
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode",
  "name": "Signposting and RO-Crate: experiences and lessons learned",
  "publisher": {
    "type": "Organization",
    "name": "Zenodo"
  },
  "size": "11.95 MB",
  "url": "https://zenodo.org/records/10847062"
}

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:citedcat="https://w3id.org/citedcat-ap/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#">
  <rdf:Description rdf:about="https://doi.org/10.5281/zenodo.10847062">
    <rdf:type rdf:resource="http://www.w3.org/ns/dcat#Dataset"/>
    <dct:type rdf:resource="http://purl.org/dc/dcmitype/Text"/>
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://doi.org/10.5281/zenodo.10847062</dct:identifier>
    <foaf:page rdf:resource="https://doi.org/10.5281/zenodo.10847062"/>
    <dct:creator>
      <rdf:Description rdf:about="https://orcid.org/0000-0001-9842-9718">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Person"/>
        <foaf:name>Soiland-Reyes, Stian</foaf:name>
        <foaf:givenName>Stian</foaf:givenName>
        <foaf:familyName>Soiland-Reyes</foaf:familyName>
        <org:memberOf>
          <foaf:Organization rdf:about="https://ror.org/https://ror.org/027m9bs27">
            <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://ror.org/027m9bs27</dct:identifier>
            <foaf:name>University of Manchester</foaf:name>
          </foaf:Organization>
        </org:memberOf>
        <org:memberOf>
          <foaf:Organization rdf:about="https://ror.org/https://ror.org/04dkp9463">
            <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://ror.org/04dkp9463</dct:identifier>
            <foaf:name>University of Amsterdam</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="https://orcid.org/0000-0002-0715-6126">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Person"/>
        <foaf:name>Van de Sompel, Herbert</foaf:name>
        <foaf:givenName>Herbert</foaf:givenName>
        <foaf:familyName>Van de Sompel</foaf:familyName>
      </rdf:Description>
    </dct:creator>
    <dct:title>Signposting and RO-Crate: experiences and lessons learned</dct:title>
    <dct:publisher>
      <foaf:Agent>
        <foaf:name>Zenodo</foaf:name>
      </foaf:Agent>
    </dct:publisher>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2024</dct:issued>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-03-21</dct:issued>
    <dct:modified rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-07-06</dct:modified>
    <owl:sameAs rdf:resource="https://zenodo.org/records/10847062"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/records/10847062</skos:notation>
        <adms:schemeAgency>URL</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation>oai:zenodo.org:10847062</skos:notation>
        <adms:schemeAgency>oai</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <dct:isVersionOf>
      <rdf:Description rdf:about="https://doi.org/10.5281/zenodo.10847061">
        <dct:identifier>https://doi.org/10.5281/zenodo.10847061</dct:identifier>
      </rdf:Description>
    </dct:isVersionOf>
    <dct:isPartOf>
      <rdf:Description rdf:about="https://zenodo.org/communities/ro">
        <dct:identifier>https://zenodo.org/communities/ro</dct:identifier>
      </rdf:Description>
    </dct:isPartOf>
    <dct:isPartOf>
      <rdf:Description rdf:about="https://zenodo.org/communities/esciencelab">
        <dct:identifier>https://zenodo.org/communities/esciencelab</dct:identifier>
      </rdf:Description>
    </dct:isPartOf>
    <dct:description>Presented at FDO Summit 2024</dct:description>
    <dcat:distribution>
      <dcat:Distribution>
        <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/>
        <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.10847062"/>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:downloadURL rdf:resource="https://zenodo.org/records/10847062/files/slides_signposting-and-ro-crate-experience-and-lessons-learned.zip"/>
        <dcat:mediaType>application/zip</dcat:mediaType>
        <dcat:byteSize>6896383</dcat:byteSize>
        <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.10847062"/>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:downloadURL rdf:resource="https://zenodo.org/records/10847062/files/signposting-and-ro-crate-experience-and-lessons-learned.pdf"/>
        <dcat:mediaType>application/pdf</dcat:mediaType>
        <dcat:byteSize>5631529</dcat:byteSize>
        <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.10847062"/>
      </dcat:Distribution>
    </dcat:distribution>
  </rdf:Description>
</rdf:RDF>

.. even different profiles of same syntax

What about APIs?

Site-specific JSON, schema must already be known
"Secret" API -- do some URL rewriting
API documented as URL patterns, e.g.
http://api.example.com/items/{item}.json
- But what is {item} ?
Links to download are often hidden behind another API call

GET http://api.example.com/item/14.json

HTTP/1.1 200 OK
Content-Type: application/json

{ "title": "Data 14", 
  "download": "http://cdn.example.net/item14.zip" }

Lots of APIs

What is Signposting?

https://signposting.org/

Provide from any Web resource (e.g. typical landing page), how to find:

Persistent identifier (how do I find it again?)
Type (what is it?)
Download links (how do I get it?)
Metadata (what is inside?)
License (can I reuse it?)
Authors (who should I credit?)

... assuming we want to do this reliably in software -- for any repository or websit

(machine actionable)

Reuse Web standards

Connect with ye olde HTTP (RFC9112 etc)
Link relations (RFC8288)
JSON (RFC8259) representation of linksets (RFC 9264)

Principles: Simplicity, navigation, (almost) no semantics

JSON

HTTP

GET http://www.example.com/repo/item/14

HTTP/1.1 200 OK 
Link: <http://cdn.example.net/item14.zip>;     rel="item"
Link: <http://api.example.com/items/14.json>;  rel="describedby"
Link: <https://doi.org/10.abcd/j.mystery.14>;  rel="cite-as"
Link: <https://schema.org/TrainingMaterial>;   rel="item"
Content-Type: text/html
Content-Length: 21398

<html>...

HTML

<html>
<head>
<link rel="stylesheet"   href="https://cdn.jsdelivr.net/npm/bootstrap..." />
<link rel="cite-as"      href="https://doi.org/10.abcd/j.mystery.14"  />
<link rel="item"         href="http://cdn.example.net/item14.zip"  />
<link rel="describedby"  href="http://api.example.com/items/14.json" />
<link rel="type"         href="https://schema.org/TrainingMaterial"   />

</head>
<body>

JSON

{ "linkset": [
  { "anchor": "http://www.example.com/repo/item/14",
    "cite-as": [
      { "href": "https://doi.org/10.abcd/j.mystery.14" }
    ],
    "item": [
      { "href": "http://cdn.example.net/item14.zip" }
    ],
    "describedby": [
      { "href": "http://api.example.com/items/14.json" }
    ]
  },
  { "anchor": "..." }
 ]
}

FAIR Signposting

Making the links meaningful

Specify the content type;

Link: <http://cdn.example.net/item14.zip>; rel="item"; type="application/zip"

Useful for alternative formats

For generic types, also specify a profile:

Link: <http:/api.example.com/marc/14>; rel="describedby";

type="application/xml";

profile="http://www.loc.gov/MARC21/slim"

Useful for JSONs with different schemas and linking to APIs

FAIR Digital Objects

A set of principles and recommendations for how to implement
FAIR across machine actionable digital objects

https://fairdo.org/

https://fairdo.org/specifications/

Conceptual FDO structure

Persistent Identifier (PID) points to a PID Record which has attributes including outgoing qualified references
FDO Type defines semantic purpose of the FDO
FDO Profile defines which attributes (and types) to expect
FDO Data points to downloadable bytes (bitstream)
Metadata beyond the attributes can be separate resources, possibly its own FDO
Registries provide common definition of attributes and profiles

https://fairdo-org.github.io/fdo-architecture-spec/

How is FDO implemented?

Several flavours available..

Broeder et al. (2024):
FDO Related Solutions (draft)

Handle system

Nanopublications

Webby FDOs

Webby FAIR Digital Objects

Recognises that Web (aka HTTP) is ubiquitous, not going away soon
Builds on existing Web standards
- Signposting for navigation (PID record)
- Linked Data for metadata
- RO-Crate as basis for metadata profiles

https://s11.no/2024/webby-fdos/

https://pypi.org/project/signposting/

$ signposting https://zenodo.org/records/13225792
Signposting for https://zenodo.org/records/13225792 
Linkset: <https://zenodo.org/api/records/13225792> application/linkset+json

$ signposting --linkset https://zenodo.org/api/records/13225792
Signposting for https://zenodo.org/api/records/13225792 
CiteAs: <https://doi.org/10.5281/zenodo.13225792>
Type: <https://schema.org/CreativeWork>
      <https://schema.org/AboutPage>
Collection: <https://zenodo.org/records/13225792>
License: <https://creativecommons.org/licenses/by/4.0/legalcode>
Author: <https://orcid.org/0000-0002-0035-6475>
        <https://orcid.org/0000-0002-4806-5140>
        <https://orcid.org/0000-0002-0048-3300>
        <https://orcid.org/0000-0003-4911-9056>
        <https://orcid.org/0000-0002-3079-6586>
        <https://orcid.org/0000-0001-9842-9718>
Describes: <https://zenodo.org/records/13225792> text/html
DescribedBy: <https://zenodo.org/api/records/13225792> application/vnd.citationstyles.csl+json
             <https://zenodo.org/api/records/13225792> text/x-bibliography
             <https://zenodo.org/api/records/13225792> application/dcat+xml
             <https://zenodo.org/api/records/13225792> application/linkset+json
             <https://zenodo.org/api/records/13225792> application/x-bibtex
             <https://zenodo.org/api/records/13225792> application/vnd.datacite.datacite+json
             <https://zenodo.org/api/records/13225792> application/vnd.inveniordm.v1.full+csv
             <https://zenodo.org/api/records/13225792> application/vnd.datacite.datacite+xml
             <https://zenodo.org/api/records/13225792> application/x-dc+xml
             <https://zenodo.org/api/records/13225792> application/vnd.inveniordm.v1+json
             <https://zenodo.org/api/records/13225792> application/vnd.inveniordm.v1.simple+csv
             <https://zenodo.org/api/records/13225792> application/vnd.geo+json
             <https://zenodo.org/api/records/13225792> application/ld+json
             <https://zenodo.org/api/records/13225792> application/json
             <https://zenodo.org/api/records/13225792> application/marcxml+xml
Item: <https://zenodo.org/records/13225792/files/d2.1-reproducible-fair-digital-objects-for-workflows.pdf> application/pdf
      <https://zenodo.org/records/13225792/files/d2.1-reproducible-fair-digital-objects-for-workflows.odt> application/octet-stream

Sandy Rogers

https://github.com/SandyRogers/signposting-chrome-extension

https://github.com/thivi19/the-fair-signposting-crawler

Thivisha Uthayakumar

References

https://signposting.org/

https://s11.no/2024/webby-fdos/

https://github.com/stain/signposting-tutorial