FIP.21.T.4 | FIP Advanced Facilitator Training - by Iseult Lynch

The Lorentz workshop on FAIR has come to an end. It was a really exciting week. So much is happening, and it's clear the first 10 years were just the beginning. I believe the next 10 years of FAIR will be even more impactful and transformative. Thanks everybody for their contributions to make such a fantastic event!

The Lorentz workshop on FAIR has come to an end. It was a really exciting week. So much is happen...

URI of the declaration of training completion nanopub

sponsor institution of the event (ROR, URL)

sponsor institution of the training (ROR, URL)

can in some situations be considered the same as

Template for defining a FAIR specification (metadata schema, metadata-data linking schema, communication protocl, knowledge representation language, structured vocabulary, semantic model and provenance model).

FAIR Implementation Community that created the resource

link to a specification that this resource implements

a link to a website with further information

Template for defining a FAIR specification:
- metadata schema,
- metadata-data linking schema,
- communication protocol,
- knowledge representation language,
- structured vocabulary,
- semantic model and
- provenance model.

Attributed to somebody and an organization

Provenance template: Attributed to somebody and an organization

MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. The database is cross-species and cross-technique and it covers metabolite structures and their reference spectra as well as their biological roles and locations. MetaboLights is the recommended metabolomics repository for a number of leading journals and ELIXIR, the European infrastructure for life science information.

figshare is a data repository where users can make all of their research outputs available in a citable, shareable and discoverable manner

Template for defining a FAIR specification for the following subtypes: metadata schema, metadata-data linking schema, communication protocol, knowledge representation language, structured vocabulary, semantic model and provenance model.

Template for defining a semantic (data) model.

specification that this resource implements

Template: Defining a Semantic (Data) Model

Template for defining a structured vocabulary.

Template: Defining a Structured Vocabulary

Template for defining a metadata schema.

FAIR Implementation Community that created this resource

Authentication and authorization service

description of the FAIR-enabling resource

Template: Defining a FAIR-enabling resource

Apache Parquet is an open source, column-oriented data file format designed for efficient data storage and retrieval. It provides efficient data compression and encoding schemes with enhanced performance to handle complex data in bulk.

This Data Station enables deposit data and search for data within the social sciences and humanities domains. The metadata of the Data Station SSH is also available in the national ODISSEI portal and the European CESSDA Data Catalogue (see the DANS website).
DANS Data Station-Social Science and Humanities (SSH)

marine mesopelagic zone - The zone of an ocean immediately below the photic zone down to a depth where the water temperature is 10degC (the thermocline).

Organism of Kiyohimea usagi Matsumoto & Robison, 1992 (species) - has habitat - marine mesopelagic zone

Kiyohimea usagi Matsumoto & Robison, 1992 (species)

coral reef - A marine reef which is composed primarily of aragonite structures produced by living organisms, found in shallow, low-nutrient waters.

Organism of Nemateleotris decora Randall & Allen, 1973 (species) - has habitat - coral reef

Nemateleotris decora Randall & Allen, 1973 (species)

The Open Science Framework (OSF) is a free and open free, open repository and platform to enable collaboration and support the entire research lifecycle: planning, execution, reporting, archiving, and discovery. Features include automated versioning, logging of all actions, collaboration support, free and unlimited file storage, registrations, and connections to other tools/services (ie. Dropbox, figshare, Amazon S3, Dataverse, GitHub). It is 100% free to researchers, open source, and intended for use in all domain areas. OSF has an open, public API to support broad indexing, as well as a partnership with Internet Archive for long-term preservation with a $250k preservation fund and an IMLS grant for transfer to Internet Archive (currently in progress). The OSF supports embargoing during peer review via a view-only link with the ability to anonymize contributor list. It also provides managed access by allowing access requests and private sharing settings. OSF is a non-profit with direct funder support through grants, government contracts, and community memberships.

has habitat - x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.

#+ endpoint: https://query.knowledgepixels.com/repo/full prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix xsd: <http://www.w3.org/2001/XMLSchema#> prefix dct: <http://purl.org/dc/terms/> select ?count ?checksum where { graph npa:graph { npa:thisRepo npa:hasNanpubCount ?count ; npa:hasNanopubChecksum ?checksum . } }

#+ endpoint: https://query.knowledgepixels.com/repo/full

prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix np: <http://www.nanopub.org/nschema#>
prefix npa: <http://purl.org/nanopub/admin/>
prefix npx: <http://purl.org/nanopub/x/>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix dct: <http://purl.org/dc/terms/>

select ?count ?checksum where {
graph npa:graph {
npa:thisRepo npa:hasNanpubCount ?count ;
npa:hasNanopubChecksum ?checksum .
}
}

Widely used for data citation, mainly used by us for collections and elaborated data products

Handle PIDs are used for all data objects at the highest possible granularity

As far as possible and provided by the persons we include ORCID ids with all personal metadata for attribution

All entries in the ICOS ontology are represented by PIDs or URIs

ePIC handles are generated to create persistent identifiers for instruments and other artefactsthat need to be persistently linked to data objects

DOIs are minted for data object that require citation, this can be documents, major higher level data products, important collections or supplemental data for scientific publications.

ePIC Handle PIDs are minted for each data object ingested at carbon portal, including collections

Services to be registered in the ENVRI Hub catalogue of services are described using the DCAT AP vocabulary using the EPOS extension. We also provide a direct mapping of ICOS metadata for L2 data objects to DCAT AP at https://meta.icos-cp.eu/sparqlclient/?q=DCAT%20metadata%20demo&type=XML

All ICOS data object landing pages have the metadata tagged in schema.org and indexed in Google Dataset search through the index page registered with Google.

All ICOS data object landing pages have the metadata available as XML encoded iso19115 through content negotiation and download button in the HTML landing page. The iso19115 XML metadata is dynamically brokered.

As defined by the CP white paper and to implement the open data sharing defined by the statutes of ICOS ERIC.

B2FIND harvested the ICOS metadata through the Datacite records for prefix 10.18160. See http://demo-b2find.cloud.dkrz.de/organization/icos

Will be implemented completely as soon as the OAI-PMH service at CP is ready, for now OpenAire indexed the ICOS data through Datacite for prefix 10.18160

All schema.org metadata from the ICOS data objects is indexed by Google Dataset Search

Dimensions indexes the ICOS Handle and Datacite prefixes

WIGOS will soon move from WMDR to WMDR2 (based on ISO19156 plus iAdopt) and as data transfer mechanism shift to WIS2. ICOS plans to follow this development.

The main faceted search data portal to find and access all ICOS and ICOS related data based on our ICOS ontology and sparql endpoint

ICOS Carbon Portal is from the start registered at re3data as community repository

Dimensions indexes and tracks citations of ICOS data objects registered at Datacite

Erddap is used as data publishing portal for the Ocean community to publish ICOS Ocean observations

open, free, and universally implementable protocol

We plan to run an instance of Viringo (https://github.com/datacite/viringo) that will serve both the ICOS Datacite DOI metadata as the iso19115 metadata from the ICOS L2+L3 products. Anyway metadata on ICOS data is harvestable through OAI-PMH through OpenAire and soon through B2FIND

The ICOS SPARQL open endpoint https://meta.icos-cp.eu/sparql serves (read-only) the complete ICOS ontology and all metadata in RDF format. It is used by most back-end and front-end services of the ICOS Carbon Portal. A GUI version is served at https://meta.icos-cp.eu/sparqlclient/

The m2m interfaces to interact with the meta and data services and other back end services are based on REST 'inspired' https calls. The calls are documented at the CP github repository at pages https://github.com/ICOS-Carbon-Portal/meta and https://github.com/ICOS-Carbon-Portal/data

Used in Jupyter hub and many other applications by the community for easy access to SPARQL, ontology, metadatahttps://pypi.org/project/icoscp/

Simple login using email address and password, confirmation of account through email, forgotten password routine with confirmation by email

For ORCID and Facebook identity providers

ORCID is a much used ID provider for researchers, using this enabling automated data sets addition to personal ORCID library of publications and data sets

Allows to federate account with many universities and RPOs

All ICOS data is available open and free.

ICOS is set up for the long term, 20-25 years starting from 2015. Statutes and data policy mention that data and metadata should be preserved also after that. In case ICOS ERIC is wound down in the future there will be a one year period to develop the contingency plan. All current landing pages generated dynamically by our metadata system can then be generated as static html pages that will together form a frozen metadata system which can be served by a simple static website at very low cost or be integrated as sub-site in another permanent website.

ICOS metadata ontology is modelled in OWL and represented in a triple store using RDF. Using our sparql endpoint metadata can be queried and results can be presented as RDF, turtle, CSV and XML. The ICOS metadata scheme is published at LOV: https://lov.linkeddata.es/dataset/lov/vocabs/cpmeta

ICOS metadata ontology is modelled in OWL and represented in a triple store using RDF. Using our sparql endpoint metadata can be queried and results can be presented as RDF, json, turtle, CSV and XML

CF-1.7 compliant netcdf metadata included in the netcdf data objects

http://meta.icos-cp.eu/ontologies/cpmeta/. The ICOS metadata scheme is also published at LOV: https://lov.linkeddata.es/dataset/lov/vocabs/cpmeta

Implemented as content negotiated XML returned for each data object landing page

As implicitly described by the ICOS statutes and formally decided by the ICOS GA in 2021

All ICOS data is licensed using the CCBY4 licence, as prescribed by the ICOS Statutes and decided by ICOS GA and described in the ICOS data policy (https://doi.org/10.18160/JDEE-PZNY)

Required for traceability and attribution to data providers

ICOS FIP 2022: This is the FIP of ICOS (representing the choices made in 2022).

prefix dbo: <http://dbpedia.org/ontology/>
prefix dbp: <http://dbpedia.org/property/>
prefix schema: <http://schema.org/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

select ?band ?album where {
?band rdf:type dbo:Band .
?album rdf:type schema:MusicAlbum .
?band dbo:genre ?_genre_iri .
?album dbp:artist ?band .
} limit 100

prefix dbo: <http://dbpedia.org/ontology/>
prefix dbp: <http://dbpedia.org/property/>
prefix schema: <http://schema.org/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

select ?band ?album where {
?band rdf:type dbo:Band .
?album rdf:type schema:MusicAlbum .
?band dbo:genre ?__genre_iri .
?album dbp:artist ?band .
} limit 100

OHDSI provides structured vocabularies and concept definitions via Athena vocabularies
OHDSI Observational Health Data Sciences and Informatics

To be findable, all compounds in TOXRIC come with a unique and persistent identifier, TAID, which is used to link the toxicology and feature data of each compound.
TOXRIC-TAID | TOXRIC Unique ID for chemicals

biophysics - study of biological systems using methods from the physical sciences

Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond.

refers to the relation (between taxon and chemical)

Such a nanopublication expresses an association between an organism taxon (e.g. a species) and a chemical.
Expressing an association between an organism taxon and a chemical

the chemical to be associated with the taxon

the type of relation between the taxon and the gene

Template: Expressing an association between an organism taxon and a chemical

Trigonostemon cherrieri - species of plant

the type of relation between the taxon and the chemical

Trigonostemon cherrieri contains trigocherrin A

refers to the relation (between taxon and gene)

association of an organism taxon to a gene

Such a nanopublication expresses an association between an organism taxon (e.g. a species) and a gene.
Expressing an association between an organism taxon and a gene

the gene to be associated with the taxon

Template: Expressing an association between an organism taxon and a gene

refers to the relation (between chemical and taxon)

Such a nanopublication expresses an association between a chemical and a taxon (e.g. a species).
Expressing an association between a chemical and a taxon

Template: Expressing an association between a chemical and a taxon

the type of relation between the chemical and the taxon

trigocherrin A in taxon Trigonostemon cherrieri

testing the new extra triples in the pubinfo part

ENES gathers the community working on Earth’s climate system modelling with the aim to accelerate progress in this field. This community is strongly involved in the assessments of the Intergovernmental Panel on Climate Change (IPCC) and provides those predictions, on which EU mitigation and adaptation policies are elaborated.
European Network for Earth System Modelling

The Swiss Personalized Health Network is a national initiative under the leadership of the Swiss Academy of Medical Sciences (SAMS). In collaboration with the SIB Swiss Institute of Bioinformatics it contributes to the development, implementation and validation of coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland.
SPHN | Swiss Personalized Health Network

Based on the INSPIRE network which supports health data from population cohorts and public health responses.

The INSPIRE infrastructure involves a number of items, which require clear descriptions and the possibility to be referenced through unique identifiers. Examples for such items include INSPIRE themes, code lists, application schemas or discovery services. Registers provide a means to assign identifiers to items and their labels, definitions and descriptions (in different languages). The INSPIRE registry provides a central access point to a number of centrally managed INSPIRE registers. The content of these registers are based on the INSPIRE Directive, Implementing Rules and Technical Guidelines.

Pubinfo template: Assign to nanopublication class

the public key with which the signing is performed

the signature element of this nanopublication

the user who signed this nanopublication

website where this nanopublication was created

Pubinfo template: Specify nanopublication type

Mus (Mus) musculus Linnaeus, 1758 (species) - has habitat - city

Mus (Mus) musculus Linnaeus, 1758 (species)

It looks like a great project; the presentation is excellent and to the point.

cites as recommended reading sense-nets-intro

PURLs are used frequently, but is not limited to it.

The assertions of a nanopublication can be considered as data.

This server is used to store nanopublications.

This server is used for sparqling nanopubs.

This server is used for creating, browsing, updating nanopublications

A discretized version of the Jeffrey's divergence with an implementation that overcomes numerical problems in rare classes

information theory - mathematical theory from the field of probability theory and statistics

Kullback–Leibler divergence - measurement of how one probability distribution is different from a second, reference probability distribution

concept drift - change of statistical properties over time

Measuring data drift is essential in machine learning applications where model scoring (evaluation) is done on data samples that differ from those used in training. The Kullback-Leibler divergence is a common measure of shifted probability distributions, for which discretized versions are invented to deal with binned or categorical data. We present the Unstable Population Indicator, a robust, flexible and numerically stable, discretized implementation of Jeffrey's divergence, along with an implementation in a Python package that can deal with continuous, discrete, ordinal and nominal data in a variety of popular data types. We show the numerical and statistical properties in controlled experiments. It is not advised to employ a common cut-off to distinguish stable from unstable populations, but rather to let that cut-off depend on the use case.
Measuring Data Drift with the Unstable Population Indicator

Department of Methodology and Statistics and Department of Cognitive Neuropsychology, Tilburg University, Prof. Cobbenhagenlaan 125, 5037 DB Tilburg, The Netherlands

Business Intelligence, University of Amsterdam, Spui 21, 1012WX Amsterdam, The Netherlands

Public Health and Primary Care, Leiden University Medical Center, Albinusdreef 2, The Netherlands

Article: Measuring Data Drift with the Unstable Population Indicator

is written by - connects an agent (left) to a thing the agent created (right)

has the text - states a comment (right) about a thing (left)

Such a nanopublication includes a text that refers to an existing resource, which could be a paper, another document, or any URL, such as stating an agreement or a correction. The reference to the existing paper is based on the Citation Typing Ontology (CiTO)., bibo and CSm ontology.

Template: Semantic social posting with CSm v0

Nanopub service: Nanopub Query at query.np.kpxl.org

Nanopub service: Nanopub Server at np.kpxl.org

Nanopub service: Nanopub Query at np.kpxl.org

agrees with - agrees with statements, ideas or conclusions presented in the cited entity

disagrees with - disagrees with statements, ideas or conclusions presented in the cited entity

discusses - discusses statements, ideas or conclusions presented in the cited entity

includes quotation from - includes one or more quotations from the cited entity

links to - provides a link, in the form of an HTTP Uniform Resource Locator (URL), to the cited entity

reviews - reviews statements, ideas or conclusions presented in the cited entity

announce event - announcing an event referred to in the URL object

announce event - announcing a job referred to in the URL object

announce resource - announcing and sharing a resource that is affiliated with the assertion creator

asks question about - asks question about about content found in the resource URL

endorses - endorses the content in the provided URL resource

listening status - assertion text describes a listening status of an audio URL

reading status - assertion text describes a reading status of a text URL

recommends - assertion recommends content in the URL

watching status - assertion text describes a watching status of a video URL

Label for agreesWith: 'agrees with - agrees with statements, ideas or conclusions presented in the cited entity' (...)

This is the original paper introducing FAIR.

Returns all referenes (in the assertion graph) of the given subject IRI.

prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix np: <http://www.nanopub.org/nschema#>
prefix npa: <http://purl.org/nanopub/admin/>
prefix npx: <http://purl.org/nanopub/x/>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix dct: <http://purl.org/dc/terms/>
prefix prov: <http://www.w3.org/ns/prov#>
prefix foaf: <http://xmlns.com/foaf/0.1/>

select ?pred ?obj ?date ?creator where {
graph npa:graph {
?np npa:hasValidSignatureForPublicKey ?pubkey .
?np dct:created ?date .
?np dct:creator ?creator .
?np np:hasAssertion ?assertion .
filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pubkey . }
}
graph ?assertion {
?_subj_iri ?pred ?obj .
}
}
order by desc(?date)

FIP.21.T.3 | FIP Facilitator training - by Andrea Tarallo

paper without obvious signs of misconduct

select the appropriate class for the paper

The URL/URI of the thing you want to comment on

Template: Positively flagging a paper/manuscript

sdata.2016.18 is a paper with confirmed first author (...)

eve-pilot-operational-data-electric-car-france is a paper without obvious signs of misconduct (...)

electrocardiogram-arrhythmia-detection-novel-signal-processing-and-persistent-homology-derived is a paper without obvious signs of misconduct (...)

benchmark-dataset-retail-multiskilled-personnel-planning-under-uncertain-demand-1 is a paper without obvious signs of misconduct (...)

short ID of manuscript (e.g. 'alpha-paper') or URI/DOI

select the organization where this work was conducted

Template: Making a manuscript declaration

Semantic micro-contributions with decentralized nanopublication services

Declaration of nanobench-paper: Semantic micro-contributions with decentralized nanopublication services

M4M.32.W.5 | PARC HBM Metadata - by Ruben Peeters

M4M.32.W.6 | PARC HBM Metadata - by Ruben Peeters

PARC Human Biomonitoring Data - by (unknown)

M4M.32.W.8 | PARC HBM Metadata - by Zdenka Bednářová

FIP15.T6 | PARC FIP1 T6 - by Barbara Magagna

FIP.15 | PARC FIP1 T2a - by Barbara Magagna

FIP.18_INT | PARC FIP2 E1 Introduction - by Barbara Magagna

FIP.18_CON1 | PARC FIP2 E2 Consultation - by Barbara Magagna

A review of an item - for example, of a restaurant, movie, or store.

Iceberg is a high-performance format for huge analytic tables. Iceberg brings the reliability and simplicity of SQL tables to big data, while making it possible for engines like Spark, Trino, Flink, Presto, Hive and Impala to safely work with the same tables, at the same time.

ITINERIS will build the Italian Hub of Research Infrastructures in the environmental scientific domain for the observation and study of environmental processes in the atmosphere, marine domain, terrestrial biosphere, and geosphere, providing access to data and services and supporting the Country to address current and expected environmental challenges. ITINERIS coordinates a network of national nodes from 22 RIs (17 from the environmental domain, 3 from agri-food with strong link with the environment and 2 from the PSE domain, supporting services for the marine domain). The participating RIs are the Italian nodes of the ESFRI Landmarks ACTRIS, EMSO, Euro-Argo, ICOS and LIFEWATCH, from the ENV domain and ANAEE from the H&F domain and closely linked to the ENV domain; the Italian nodes of the ESFRI projects DANUBIUS, DISSCO, e-LTER, from the ENV domain, and EMPHASIS and EUIBISBA from the H&F domain and also relevant for ENV; the EU RIs ECORD, EUFAR, Eurofleets, JERICO and SIOS, all from the ENV domain; and the national RIs ATLAS, CeTRA, Laura Bassi, and SMINO, from the ENV domain, and Geosciences and LNS, both from the PSE domain, that in ITINERIS support services in the marine domain. The main goal is to develop cross-disciplinary research in environmental sciences through the use and re-use of existing (or pre-operational) data and services and new observations, to address scientifically and societally relevant issues such as sustainable use of natural resources, implementation of Nature-Based Solutions, Green and Blue Economy, pollution reduction, critical zone and ecosystem management and restoration, carbon cycle, mitigation of the downstream effects of climate and environmental change. This broad-scale vision of environmental research, sustained by the main Italian environmental scientists involved in European RIs, is truly innovative and it will support our Country in taking a leading role in European environmental research, designing the framework for the next decades.
ITINERIS | Italian Integrated Environmental Research Infrastructures System

The ITINERIS Hub is the unified access point to Italian environmental facilities, FAIR data and related services. Through the ITINERIS HUB all users have access to data and services, with a proper access management system and a complete catalogue of data and services. ITINERIS will not develop a new Data Center, but rather harmonize the already existing ones, which will be reinforced by the project activities. Most of the data-related activities will be devoted to reach the most appropriate level of FAIRness for all the involved RIs. The Catalogue will contain metadata that describes the research, providing available direct access to the underlying data collections or specific data portals where research data and products could actually be retrieved

FIP.21.T.2 | FIP facilitator training - by Shuai Wang

The NERC Vocabularies are a standardised lists of terms and taxonomies related to a wide range of concepts which are used to facilitate data markup, interoperability and discovery in the marine and associated earth science domains accessible via the NVS service. Some of these vocabularies are totally managed by BODC, others are managed by BODC on behalf of other organisations, while some are owned and, when relevant, managed by external governance authorities.

ORCID identifier of the person who performed the formalization

Provenance template: Generated by a NLP facilitated activity

has keywords - Relevant keyword for this post

Such a nanopublication includes a text that refers to an existing resource, which could be a paper, another document, or any URL, such as stating an agreement or a correction. The reference to the existing paper is based on the Citation Typing Ontology (CiTO)., schema.org and CoSMO - Common sensemaking ontology.

The NVS service provides access to standardised lists of terms and taxonomies related to a wide range of concepts which are used to facilitate data markup, interoperability and discovery in the marine and associated earth science domains. Some of these vocabularies are totally managed by BODC, others are managed by BODC on behalf of other organisations, while some are owned and, when relevant, managed by external governance authorities.

-----BEGIN PUBLIC KEY-----
MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAoWenJzEuzPmfkMRSKSwC
flfKiFtZOzacYCEF6/CSHmpWQRN/zqsOXbIWUM+l/ePd8Cj7eBPpEX7XFZyhSK6E
mNAWmn2/i7RsJI9El1YUDgeI7Re3BV1ZSja09b8oFAqkyI3QMK23M4D/l/hg/L1h
7PMamUj+zZL4mP+x+bnX+gxezjfodZrNZhJO4JtK8INFo3AHTEUYakWSl1KV6veW
okccyEWhThaNSK7QnnS2Eyfb2lLsKqYYi+CtIdX2ANnLFprVN33VvKpSoliM8J4Z
QtK4JOEmWYA1md+2Sp1VDHNykmuJuwLwBzp3V0fu29egfoPv8/o1rR8KNJToyPFh
SQIDAQAB
-----END PUBLIC KEY-----

This account controls the RSA public key: -----BEGIN PUBLIC KEY-----
MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAoWenJzEuzPmfkMRSKSwC
flfKiFtZOzacYCEF6/CSHmpWQRN/zqsOXbIWUM+l/ePd8Cj7eBPpEX7XFZyhSK6E
mNAWmn2/i7RsJI9El1YUDgeI7Re3BV1ZSja09b8oFAqkyI3QMK23M4D/l/hg/L1h
7PMamUj+zZL4mP+x+bnX+gxezjfodZrNZhJO4JtK8INFo3AHTEUYakWSl1KV6veW
okccyEWhThaNSK7QnnS2Eyfb2lLsKqYYi+CtIdX2ANnLFprVN33VvKpSoliM8J4Z
QtK4JOEmWYA1md+2Sp1VDHNykmuJuwLwBzp3V0fu29egfoPv8/o1rR8KNJToyPFh
SQIDAQAB
-----END PUBLIC KEY-----

Delta Lake is an open-source storage framework that enables building a Lakehouse architecture with compute engines including Spark, PrestoDB, Flink, Trino, and Hive and APIs for Scala, Java, Rust, and Python. It is built on top of Apache Parquet.

A team of builders is developing the Sensemaking network, a new interoperable, humancentric social network.

Template: Semantic social posting with CSm test

Interesting library for structured parsing for LLMs

-----BEGIN PUBLIC KEY-----
MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAimMmND/P29erWCzdNJlb
KdnS1Bx683/8Om0XT8QuYeeZnBusG0XjmlXSBAeD/G0JQOxeGH81unJcWyh/NA2L
vRn5n71HDTEmLXKC+vOzLzctytlmQFTIiTK85S/8h8NaYd8e+zrCO5pfeIcoiL84
IxFvEYmTdwxE/agkAi6We10OEyFoveJ/eiXTTec+d13IcAYjaI+F8TlRqsxdXPhy
hUs/DbX/X3fq2F0eLvXQNtL6Z2QprRw7ecFkW21EsSp876YoLy2bNKLLG+YMfDEe
HeCkr/U6IgLzQss0afkEXvLPgT4EYqt4E+/+icSDmCG0hq+oCGRXY51+jR1uVnh8
DwIDAQAB
-----END PUBLIC KEY-----

This account controls the RSA public key: -----BEGIN PUBLIC KEY-----
MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAimMmND/P29erWCzdNJlb
KdnS1Bx683/8Om0XT8QuYeeZnBusG0XjmlXSBAeD/G0JQOxeGH81unJcWyh/NA2L
vRn5n71HDTEmLXKC+vOzLzctytlmQFTIiTK85S/8h8NaYd8e+zrCO5pfeIcoiL84
IxFvEYmTdwxE/agkAi6We10OEyFoveJ/eiXTTec+d13IcAYjaI+F8TlRqsxdXPhy
hUs/DbX/X3fq2F0eLvXQNtL6Z2QprRw7ecFkW21EsSp876YoLy2bNKLLG+YMfDEe
HeCkr/U6IgLzQss0afkEXvLPgT4EYqt4E+/+icSDmCG0hq+oCGRXY51+jR1uVnh8
DwIDAQAB
-----END PUBLIC KEY-----

This is an interesting paper - https://arxiv.org/abs/2312.05230

This is an interesting paper https://arxiv.org/abs/2312.05230

announce job - announcing a job referred to in the URL object

endorses - endorses the content, statement, or any object in the provided URL resource

listening status - post text describes a listening status of an audio URL

reading status - post text describes a reading status of a text URL

recommends - the post recommends content in the URL

watching status - post text describes a watching status of a video URL

Watch out with the semantic web. It's coming for you.

A workflow to qualify FAIR Supporting Resource (FSR) records. Enables Go FAIR facilitators to verify that a FSR record is well defined (and to improve it if not). Qualified resources display the GFF tick mark in the FIP Wizard.

This looks interesting https://www.smarter-together.org/

Added to my reading list!

https://philarchive.org/rec/FIGWAW

Looking forward to reading this

https://philarchive.org/rec/FIGWAW

Looks interesting

https://arxiv.org/abs/2402.12422

I think this idea is true http://google.com

The architecture of the dataset schema fits with the metadata that we wish to create for our resource.

The architecture of the data base matching the data schema.

We want to provide an unrestricted access to the data

PandemicPACT FIP: This is the FIP of PandemicPACT

product demonstration - demonstration of a product to potential customers or others

think this is underrated: product demonstration

Organism of Rattus rattus (species) - has habitat - city

FA.2.1 | GO FAIR Austria FAIR Awareness Day 1 - by Barbara Magagna

M4M.28.T5 | PARC M4M Schema Training 5 - by Barbara Magagna

FA 2.2 | GO FAIR Austria FAIR Awareness Day 2 - by Barbara Magagna

FAIR-Supporting resource to be developed

description of the FAIR-Supporting Resource

the name of the FAIR-Supporting Resource

This is an excellent read https://arxiv.org/abs/2401.11817

This is the authentication and authorization service for the Center for Expanded Data Annotation and Retrieval (CEDAR) Workbench.

This is an interesting read, highly recommended!

https://arxiv.org/abs/2401.11817

I really enjoyed this paper https://arxiv.org/abs/2312.05230

I love Donald https://www.donaldjtrump.com/

FIP.22.T1 | WorldFAIR FIP Facilitator Training - by Iseult Lynch

scholarly paper - any kind of scholarly work, such as an article, book, etc.

DOI (https://doi.org/10...) or other URL of the citing article

Such a nanopublication expresses citation relations of a given article based on the CiTO relation types.

DOI (https://doi.org/10...) or other URL of the cited article

cites - The citing entity cites the cited entity, either directly and explicitly (as in the reference list of a journal article), indirectly (e.g. by citing a more recent paper by the same group on the same topic), or implicitly (e.g. as in artistic quotations or parodies, or in cases of plagiarism).

cites as authority - cites as something that provides an authoritative description or definition of the subject under discussion

cites as data source - cites as source of data

cites as evidence - cites as source of factual evidence for statements it contains

cites as metadata document - The citing entity cites the cited entity as being the container of metadata describing the citing entity.

cites as potential solution - cites as providing or containing a possible solution to the issues being discussed

cites as recommended reading - cites as an item of recommended reading

cites as related - cites as something that is related

cites as source document - cites as being the entity from which the citing entity is derived, or about which the citing entity contains metadata

cites for information - cites as a source of information on the subject under discussion.

compiles - The citing entity is used to create or compile the cited entity.

confirms - confirms facts, ideas or statements presented in the cited entity

contains assertion from - contains a statement of fact or a logical assertion originally present in the cited entity

corrects - corrects statements, ideas or conclusions presented in the cited entity

credits - acknowledges contributions made by the cited entity

critiques - critiques statements, ideas or conclusions presented in the cited entity

derides - The citing entity express derision for the cited entity, or for ideas or conclusions contained within it

disputes - disputes statements, ideas or conclusions presented in the cited entity

documents - documents information about the cited entity

extends - extends facts, ideas or understandings presented in the cited entity

includes excerpt from - The citing entity includes one or more excerpts from the cited entity.

obtains background from - The citing entity obtains background information from the cited entity.

obtains support from - The citing entity obtains intellectual or factual support from the cited entity.

parodies - The citing entity imitates the characteristic style or content of the cited entity for comic effect, usually without explicit citation.

plagiarizes - A property indicating that the author of the citing entity plagiarizes the cited entity, by including textual or other elements from the cited entity without formal acknowledgement of their source. The citing entity thus contains no explicit citation of the cited entity, according to the norms of scholarly practice, but cites it implicitly.

qualifies - qualifies or places conditions or restrictions upon statements, ideas or conclusions presented in the cited entity

refutes - refutes statements, ideas or conclusions presented in the cited entity

replies to - replies to statements, ideas or criticisms presented in the cited entity

retracts - The citing entity constitutes a formal retraction of the cited entity.

ridicules - The citing entity ridicules the cited entity or aspects of its contents.

speculates on - speculates on something within or related to the cited entity, without firm evidence

supports - provides intellectual or factual support for statements, ideas or conclusions presented in the cited entity

updates - updates statements, ideas, hypotheses or understanding presented in the cited entity

uses conclusions from - describes work that uses conclusions presented in the cited entity

uses data from - describes work that uses data presented in the cited entity

uses method in - describes work that uses a method detailed in the cited entity

This article rocks https://arxiv.org/abs/2312.05230

Looking forward to this event https://scios.desci.community/

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We (CSm) are presenting in this awesome event! Come join us https://scios.desci.community

I cannot overstate how much I loved working with https://www.osmosistranslations.com

This was a really cool paper https://www.biorxiv.org/content/10.1101/2023.06.27.546708v1

We are working on an FDO ecosystem for Germany.

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this is a cool project!

https://www.osmosistranslations.com/

Cool work by https://www.osmosistranslations.com/

Disable here https://twitter.com/settings/connected_apps/26368336

BioSamples, previously the BioSample Database (BioSD), stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Samples are either 'reference' samples (e.g., from 1000 Genomes, HipSci, FAANG) or have been used in an assay database such as the European Nucleotide Archive (ENA) or ArrayExpress. It provides links to assays and specific samples, and accepts direct submissions of sample information.

this looks interesting https://philpapers.org/rec/ICHECZ

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You should try https://osmosistranslations.com whenever you need top-level translation services. Trust me.

highly recommended read https://philpapers.org/rec/ICHECZ

What do you think about this? I think we should try to talk about this more https://www.dea.gov/sites/default/files/2020-06/Psilocybin-2020.pdf

This is a long post with a text to https://osmosistranslations.com it is really good and you should try it

Lorem ipsum, or lipsum as it is sometimes known, is dummy text used in laying out print, graphic or web designs. The passage is attributed to an unknown typesetter in the 15th century who is thought to have scrambled parts of Cicero's De Finibus Bonorum et Malorum for use in a type specimen book. It usually begins with:

“Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.”

The purpose of lorem ipsum is to create a natural looking block of text (sentence, paragraph, page, etc.) that doesn't distract from the layout. A practice not without controversy, laying out pages with meaningless filler text can be very useful when the focus is meant to be on design, not content.

The passage experienced a surge in popularity during the 1960s when Letraset used it on their dry-transfer sheets, and again during the 90s as desktop

this is an interesting paper https://www.bmj.com/content/384/bmj-2023-077310

check out this great research https://philpapers.org/rec/ICHECZ

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The Sussex Centre for Consciousness Science @SussexCentre is one of the @SussexUni's 12 new Centres of Excellence. And we have a bunch of open positions right now: https://www.sussex.ac.uk/research/centres/sussex-centre-for-consciousness-science/people/join-us

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SciOS is happening now! Come on down to learn about how FAIR Data and AI can help science.

We're here at the #descisummit with @rtk254 as he demos the commonsensemaker's social nanopublication app. Imagine - this tweet is completely machine-actionable - no more losing academic data behind X's API paywall.

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Who in my network is interested in data ownership?

Presented ARCs and Attestations MVP for DeSci Nodes at SciOS. Like me, it is scrappy but promising. Next step is to synthesise knowledge about stigmergy and designing online communities with other speakers like Ronen, whose paper shaped our thinking immensely https://arxiv.org/abs/2205.06345

We're at the #descisummit at Eth Denver with @rtk254 learning about social nanopublications! Imagine this tweet is fully machine readable - no more losing academic discourse behind x's API paywall.

Check out more here: https://csensemakers.com/

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I was very excited to join my first DeSci event today. Learning more about FAIR data, semantics and their implementations in a decentralized world. Unfortunately I am leaving today and cannot stay after the FAIR workshop, but wanted to share some links to relevant work and communities I am working in around Open Source technologies for Agriculture : Regen Network data module https://docs.regen.network/modules/data/01_concepts.html and OpenTEAM https://openteam.community/

M4M.32.W.9 | PARC HBM Metadata - by Zdenka Bednářová

is a - asserts that the thing on the left belongs to the class on the right

is called - connects a formal identifier (left) to an informal human-readable name (right)

is a subclass of - states that all instances of the class to the left are also instances of the class to the right

class - a class represents a set of concrete or abstract things

is defined as follows: - connects an identifier (left) to a human-readable definition (right)

is related to - connects two classes that are somehow related

Such a nanopublication defines a new class. Classes represent sets of concrete or abstract things, and are by convention named with singular nouns (or noun phrases) like 'human', 'cardiovascular disease', or 'approach'.

If the term you want to define does not refer to a set of things but a single instance, such as the planet Mars or Marie Curie, define them with the template for individuals instead.

URI of a class that should be treated as fully synonymous

Nanopub service: Nanopub Query at sdsc.edu

I’m DeSci-ing in Denver! Come join 👩‍🔬

2/27 10:20 at SciOs24

2/27 2:12 at AuraNova

3/1 DeSci Summit at CU

My talks will center on data standardization, @MuseMatrix_, & @DeSciResearch

To explore more awesome DeSci happenings in Denver go to

➡️ https://denver.desci.community/

@descieth

FIP.23.W.1 | CLARIAH FIP workshop - by Shuai Wang

DDI-Lifecycle is designed to document and manage data across the entire life cycle, from conceptualization to data publication, analysis and beyond. It encompasses all of the DDI-Codebook specification and extends it. Based on XML Schemas, DDI-Lifecycle is modular and extensible. This version also supports improvements in Classification management (based on GSIM / Neuchatel), non-survey data collection (Measurements), sampling, weighting, questionnaire Design and support for DDI as a Property Graph.

This license is for the LISS (Longitudinal Internet studies for the Social Sciences) panel.

FIP.24.W.1 | GLOBALISE FIP workshop - by Angelica Maineri

FIP.19_FCM | PARC_FAIR Convergence - by Barbara Magagna

I really liked this blog post! https://paragraph.xyz/@sense-nets/sense-nets-intro

✨ Our Dept is hiring MANY scholars this year ✨Full list of the many roles I mentioned the other day now in one place! https://www.jobs.ac.uk/enhanced/linking/kings-college-london-digital-humanities-feb-2024/ Come join me and my colleagues at @kingsdh! Several with focus on the Global South/Southeast Asia!

https://arxiv.org/abs/2312.05230 interesting paper, connecting language models to agent models

PARC | Partnership for the Assessment of Risks of Chemicals - by (unknown)

FIP.25.T.1 | FIP.25 PARC training - by (unknown)

M4M.29.T.3 | M4M Vocabulary Training for PARC 3 - by Katarína Řiháčková

FIP.25.T.1 | FIP.25 PARC training - by Parul Tewatia

Organism of Ophonus (genus) - preys on - organism of Apiaceae (family)

At the moment there is only one direction link - metadata link to data

Not yet implemented - will be a institutional platform

Copy of ADVANCE FIP: This is the FAIR Implementation profile of the ADVANCE project within the scope of the Helmholtz Metadata Collaboraion

This is a cool paper! https://arxiv.org/abs/2402.04607

I really liked this paper! Highly recommended https://arxiv.org/abs/2402.04607

participated as facilitator assistant in

Declaring the completion of a 3PFF Programme

Template: Declaring the completion of a 3PFF Programme

this paper is really nice https://arxiv.org/abs/2402.04607

alpine tundra ecosystem - A tundra ecosystem which exists at high altitudes and where vegetation is stunted due to low temperatures and high winds.

Organism of Leistus (Pogonophorus) punctatissimus Breit, 1914 (species) - has habitat - alpine tundra ecosystem

Leistus (Pogonophorus) punctatissimus Breit, 1914 (species)

I really recommend this paper, recently read it and learned a lot! https://arxiv.org/abs/2402.04607

✨ Our Dept is hiring MANY scholars this year ✨Full list of the many roles I mentioned the other day now in one place!

Come join me and my colleagues at @kingsdh! Several with focus on the Global South/Southeast Asia!

I am a bit confused about this paper. It talks about the relation between causation and mechanism, but seems to shy away from defining causation. It does not mention the big epistemic problem of causation (confounding) once. I think we need definitions for clarity.

https://www.nature.com/articles/s41583-023-00778-7

nanopublication - A small knowledge graph snippet with metadata that is to be treated as an independent (scientific) publication.

think this is underrated: nanopublication

Organism of Picus viridis (species) - has habitat - city

Nebria germarii Heer, 1837 (species) - has habitat - alpine tundra ecosystem

Nebria diaphana Daniel & Daniel, 1890 (species) - has habitat - alpine tundra ecosystem

Nebria diaphana Daniel & Daniel, 1890 (species)

FIP.25.T.2 |PARC FIP Training - by Parul Tewatia

Nebria germarii Heer, 1837 (species) - preys on - Collembola (class)

The Ocean InfoHub aims to build a sustainable, interoperable, and inclusive digital ecosystem for all Ocean data centres. Existing and emerging data systems are linked, with the ultimate goal of coordinating action and capacity to improve access to Ocean data and knowledge.
WF-Oceanography | WorldFAIR WP11 Oceanography Community

Nebria germarii Heer, 1837 (species) - preys on - Pardosa (genus)

Nebria germarii - associated with - Trechus dolomitanus

FIP.25.T.3 | PARC Facilitator Training - by David Schott

This is a community created to describe the trainees of the Partnership for Assessment of Risk from Chemicals Community participating GFF 3PFF training sessions.
PARCTrain | Partnership for Assessment of Risk from Chemicals Training Community
PARCTrain | Partnership for Assessment of Risk from Chemicals Training Community - by (unknown)

The IISH maintains a large collection of datasets, which are stored in Dataverse, an open-source repository system shared by a large number of institutions around the world. By storing our data in Dataverse, we adhere to the community-driven principles of FAIR data, ensuring that IISH data is findable, accessible, interoperable and reusable. There are 25 instances of Dataverse for various projects.

Fascinating and important - and seems very plausible to me👇

https://www.cambridge.org/core/journals/behavioral-and-brain-sciences/article/reconsidering-the-link-between-past-material-culture-and-cognition-in-light-of-contemporary-huntergatherer-material-use/A121ADFA3627FE054641F13FA2E20E05

M4M.26.INT1| PARC M4M Introduction event 1 - by Barbara Magagna

Nanopublication setting: first nanopublication setting

Nebria germarii - related to - Trechus dolomitanus

parasitoid of - A parasite that kills or sterilizes its host

has parasitoid - inverse of parasitoid of

obligate parasite of - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.

facultative parasite of - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.

stem parasite of - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)

root parasite of - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)

hemiparasite of - A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.

biotically interacts with - An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.

trophically interacts with - An interaction relationship in which the partners are related via a feeding relationship.

preys on - An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members

symbiotically interacts with - A biotic interaction in which the two organisms live together in more or less intimate association.

commensually interacts with - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).

mutualistically interacts with - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).

interacts with via parasite-host interaction - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).

participates in a abiotic-biotic interaction with - A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.

hyperparasite of - x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y

hyperparasitized by - inverse of hyperparasite of

participates in a biotic-biotic interaction with

ectoparasite of - A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host

has ectoparasite - inverse of ectoparasite of

mesoparasite of - A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite

has mesoparasite - inverse of mesoparasite of

intercellular endoparasite of - A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.

has intercellular endoparasite - inverse of intercellular endoparasite of

intracellular endoparasite of - A sub-relation of endoparasite-of in which the parasite inhabits host cells.

has intracellular endoparasite - inverse of intracellular endoparasite of

epiphyte of - An interaction relationship wherein a plant or algae is living on the outside surface of another plant.

kleptoparasite of - A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material

kleptoparasitized by - inverse of kleptoparasite of

lays eggs on - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.

has eggs laid on by - inverse of lays eggs on

Label for RO_0002208: 'parasitoid of - A parasite that kills or sterilizes its host' (...)

refers to - links an association to its object

refers to the relation (between subject taxon and object taxon)

refers to - links an association to its subject

refers to the object taxon's life cycle stage

refers to the subject taxon's life cycle stage

has the name - links a taxon usage to a taxon name

Such a nanopublication expresses an association between classes of organisms (taxa), a subject taxon and an object taxon, for example expressing that the organisms of the subject taxon prey on organisms of the object taxon.

For expressing observations of interactions between individual organisms, please use the alternative template "Associations between organisms".

Expressing an association between two organism taxa
${subjtaxonname} - ${relation} - ${objtaxonname}

short explanation related to the above statement

the life cycle stage of the object taxon

publication DOI (https://doi.org/...) or taxon treatment ID (https://treatment.plazi.org/id/...)

search and select from list (if not found, you may paste URL from IPNI, MycoBank, Index Fungorum, or ZooBank)

the type of relation between the two taxa

the life cycle stage of the subject taxon

search and select from list (if not found, paste identifying URI from IPNI, MycoBank, Index Fungorum, or Zoobank)

Template: Expressing an association between two organism taxa

Nebria germarii Heer, 1837 (species) - ecologically co-occurs with - Trechus (Trechus) dolomitanus Jeannel, 1931 (species)

Trechus (Trechus) dolomitanus Jeannel, 1931 (species)

Trechus (Trechus) dolomitanus Jeannel, 1931 (species) - has habitat - alpine tundra ecosystem

Leistus (Pogonophorus) punctatissimus Breit, 1914 (species) - has habitat - alpine tundra ecosystem

This is an important paper https://arxiv.org/abs/2402.04607

Canis lupus lupus (subspecies) - preys on - Mus (Mus) musculus Linnaeus, 1758 (species)

Exchangeable image file format is a standard that specifies formats for images, sound, and ancillary tags used by digital cameras, scanners and other systems handling image and sound files recorded by digital cameras. This resource represents version 2 (the linked standard is version 2.32).
EXIF 2 | Exchangeable Image File Format version 2

Exchangeable image file format is a standard that specifies formats for images, sound, and ancillary tags used by digital cameras, scanners and other systems handling image and sound files recorded by digital cameras. This resource represents version 3.
EXIF 3 | Exchangeable Image File Format version 3

decentralization - process of redistributing or dispersing functions, powers, people or things away from a central location or authority

think this is underrated: decentralization

semantic publishing - publishing on the Semantic Web

think this is underrated: semantic publishing

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This account controls the RSA public key: -----BEGIN PUBLIC KEY-----
MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkZqFrE/i7b0Uwvf03Al9
ijLd2B2lczvDoTj6Nw3K3odcyzt04ojVGn6MJOgjxZGpneIJpT5X7RqUfUSe3KvU
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DNaFtaMchnaFIXdjCHMFhnfKX2jwzUtqVOajvA9IghZBLIjZU1uTHfCtL91OibeU
vwIDAQAB
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Interesting essay https://scholarlykitchen.sspnet.org/2021/08/24/unpacking-the-altmetric-black-box/

And on that note, I'm also hiring applied researchers with a penchant for muddling through complex problem spaces and a deep interest in co-operative ecosystems. Skills in text embeddings, discourse analysis and protocol-thinking a plus, but at this stage, mostly looking for folks who enjoy synthesizing and identifying common threads. Please share with your network if it might be a good fit! https://v6acolab.org/Work-With-US

I've just spent a pleasant half hour leafing through Michel Talagrand's "What is a Quantum Field Theory?"

https://www.amazon.com/What-Quantum-Field-Theory-Mathematicians/dp/1316510271

I suspect this is a book that would repay close study, even for many people who know quantum field theory much better than I ever did (though maybe not true experts?). At quite a few points I found myself thinking "oh, that's very well put!", which is usually a sign a textbook is worth engaging with!

I don't plan to study this in depth - I looked at it because of Talagrand winning the Abel Prize today - but it was a lot of fun to look!

This ontology contains entities such as: datatype, datatype generator, datatype quality and others giving the possibility to represent arbitrary complex datatypes. This is an important fact for a general data mining ontology that wants to represent and query over modelling algorithms for mining structured data. The ontology was first developed under the OntoDM (Ontology of Data Mining is available at http://kt.ijs.si/panovp/OntoDM) ontology, but for generality and reuse purpose it was decided to export it as a separate ontology. Additionally, the OntoDT ontology is based on and ISO/IEC 11404 (http://www.iso.org/iso/catalogue_detail.htm?csnumber=39479) standard and can be reused used independently by any domain ontology that requires representation and reasoning about general purpose datatypes.

BioPortal is a repository of biomedical ontologies—the largest such repository, with more than 300 ontologies to date. This set includes ontologies that were developed in OWL, OBO and other formats, as well as a large number of medical terminologies that the US National Library of Medicine distributes in its own proprietary format.

"In a potential future world of #FAIR (Findable, Accessible, Interoperable, & Reusable) science, every research artifact – not just the published manuscript – will need a globally unique, persistent, & resolvable identifier. Trillions of #PIDs must be minted over the next decade to achieve that goal, & trillions of PID-to-URL mappings will need to be maintained. This is inconceivable with the current #DOI system." https://scholarlykitchen.sspnet.org/2024/03/14/guest-post-navigating-the-drift-persistence-challenges-in-the-digital-scientific-record-and-the-promise-of-dpids/

M4M.33.T.1 | PARC Trainer training - by Panče Panov

has the description - attaches a human-readable description (right) to a formal identifier of a thing (left)

is a - links a thing (left) to a class it belongs to (right)

has the name - attaches a human-readable name (right) to a formal identifier of a thing (left)

Nanopublication service type: ${servicetype}

a textual description of the service type

the higher-level entity of which this is a more specific version of

short ID of service type - this is the identifier of the service type

Template: Defining a nanopublication service type

Second-generation query service for nanopublications.

Nanopublication service type: nanopub-query

Version 1.0 of Nanopub Query, the second-generation query service for nanopublications

Nanopublication service type: nanopub-query-1.0

Version 1.1 of Nanopub Query, the second-generation query service for nanopublications

Nanopublication service type: nanopub-query-1.1

Frontiers for Young Mind article to introduce budding scientists on the story of Sir James Black, reknowned pharmacologist. The cited article provides detail on how his work brought about rational drug design

The Open Research Knowledge Graph (ORKG) is a digital scholarship infrastructure for the production, curation, publication and use of FAIR scientific knowledge. Its mission is to shape a future scholarly publishing and communication where the contents of scholarly articles are FAIR research data.

Nanopub service: Nanopub Query at knowledgepixels.com

Nanopub service: Nanopub Query at np.trustyuri.net

Nanopublication service type: nanodash-2.x

Nanopub service: Nanodash at knowledgepixels.com

Nanopub service: Nanodash at petapico.org

Nanopub service: Nanodash at np.trustyuri.net

definition - statement of the meaning of a word or phrase

Philaenus signatus Melichar, 1896 (species) - has host - Asphodeline lutea (L.) Rchb. (species)

Philaenus signatus Melichar, 1896 (species)

Standard International Trade Classification (SITC) is a classification of goods used to classify the exports and imports of a country to enable comparing different countries and years. The classification system is maintained by the United Nations. The SITC classification, is currently at revision four, which was promulgated in 2006 (source Wikipedia: https://en.wikipedia.org/wiki/Standard_International_Trade_Classification).
SITC | Standard International Trade Classification

The Art & Architecture Thesaurus (AAT) is a structured vocabulary for describing and indexing the visual arts and architecture.

The Cultural Heritage Thesaurus (CHT) contains concepts that cover the field of cultural heritage in the Netherlands. It is maintained by the National Cultural Heritage Agency (Rijksdienst voor het Cultureel Erfgoed).

The Australian National University (ANU) conducted the ESS in an Australian context, under the title of the Australian Social Survey International – ESS (AUSSI-ESS). The purpose of the Australian study was to conduct a national study that enabled cross-continent comparisons to European countries that participate, to better understand the similarities and differences between countries. The fieldwork methodology for AUSSI-ESS was completed using self-completion of surveys via the web. This was different to that traditionally used in the ESS, which had used face-to-face survey methods almost exclusively through Wave 9.
Australian Social Survey International – European Social Survey (AUSSI-ESS)
AUSSI-ESS | Australian Social Survey International – European Social Survey

SPSS, Stata, SAS, R, CSV are being used. But they are not considered KR languages. Thus removed in this version.

Australian Social Survey International-ESS (AUSSI-ESS)

FAIR Supporting Resource to be developed

Template for defining an authentication and authorization service.
Defining an Authentication and Authorization Service

Template: Defining an Authentication and Authorization Service

Template for defining an identifier service.

Template: Defining an Identifier Service

GLOBALISE is a project of the Huygens Institute with the International Institute of Social History, the Digital Infrastructure Department of the KNAW Humanities Cluster, VU University, the University of Amsterdam, and the Dutch National Archives. It is funded by the Dutch Research Council (NWO), grant no. 175.2019.003. Committed to enhancing the accessibility and research potential of the UNESCO Memory of the World-listed Dutch East India Company (VOC) archives, GLOBALISE has transcribed over 5 million handwritten pages and applies state-of-the-art AI methods to extract key entities, such as persons and places, as well as events from the texts. Reference data from secondary sources, collected and curated by project members, provides context to the entities and events.

The LISS Data Archive contains three main sources of data. The Background variables contain monthly-updated socio-economic and demographic information. The LISS Core Study is an annual longitudinal survey consisting of multiple questionnaires covering a broad range of topics. The Assembled Studies contain surveys and experiments conducted as paid or externally funded assignments. You can browse studies and download codebooks and datasets. Each dataset contains the variable ‘nomem_encr’ with unique panel member IDs, which can be used to merge datasets together.

The LISS data archive community is the community of LISS panel that work on high-quality online research infrastructure in the Netherlands. All data obtained by studies in the LISS panel are published on the LISS Data Archive website.

This conversation between

@balazskegl

and

@yoginho

is a follow-up to my discussion on the same podcast about our "Naturalizing Relevance Realization" paper and much more. Excellent to listen to! (just doing so right now but it is already apparent ;) ). https://www.youtube.com/watch?v=5UJ4y2L2qpk

The activity of sharing a web link that one finds useful, so others can find out about it and possibly up-/down-vote it.

Class: The activity of sharing a web link

the title of the document (possibly edited)

Open Data Infrastruktur für die Biodiversität

Open Science Retreat #2: CiTO Nanopublications

"Open Data Infrastruktur für die Biodiversität"

"Open Science Retreat #2: CiTO Nanopublications"

The Ocean InfoHub (OIH) federated metadata handling system relays the metadata PIDs (given to JSON-LD records) from our partners. The PID services used are diverse, including PURLs run by trusted and sustained organisations (e.g. OBO Foundry), DOIs, W3IDs, and IDs issued by trusted aggregators (e.g. OBIS). Not all metadata records integrated into our knowledge graph are assigned PIDs, a scenario we are gradually changing now that metadata records exist for use in Ocean InfoHub and ODIS

The ODIS Catalogue of Sources aims to be an online browsable and searchable catalogue of existing ocean related web-based sources/systems of data and information as well as products and services. It will also provide information on products and visualize the landscape (entities and their connections) of ocean data and information sources.
ODIS: IOC Ocean Data and Information System Catalogue of Sources

The Ocean Biodiversity information System (OBIS) seeks to absorb, integrate, and assess isolated datasets into a larger, more comprehensive pictures of life in our oceans. The system hopes to stimulate research about our oceans to generate new hypotheses concerning evolutionary processes, species distributions, and roles of organisms in marine systems on a global scale. The abstract maps that OBIS generates are maps that contribute to the ‘big picture’ of our oceans: a comprehensive, collaborative, world-wide view of our oceans. OBIS provides a portal or gateway to many datasets containing information on where and when marine species have been recorded. The datasets are integrated so you can search them all seamlessly by species name, higher taxonomic level, geographic area, depth, and time; and then map and find environmental data related to the locations.
OBIS | Ocean Biodiversity Information System

declares planned replacement of
Connects a FIP declaration to the resource that the community thereby declares to plan to replace in the future. The same declaration should also state a resource that the community declares to plan to use instead (with fip:declares-planned-use-of).

declares planned development of
Connects a FIP declaration to the resource that the community thereby declares to plan to develop

declared for digital object type
Connects a FIP declaration to the digital object type it applies to

considerations
Considerations that led to a given FIP declaration

Available FAIR-Enabling Resource
A FAIR-enabling resource that is available for use

FAIR-Enabling Resource to be Developed
A FAIR-enabling resource that is not yet available but still needs to be developed

declared by
Connects a FIP declaration to the community that made the declaration

declares current use of
Connects a FIP declaration to the resource that the community thereby declares to currently use

declares planned use of
Connects a FIP declaration to the resource that the community thereby declares to plan to use in the future

declared for case study
Connects a FIP declaration to the case study it refers to.

Nanopublications representing the FAIR Implementation Profiles (FIP) Ontology

The purpose of W3ID is to provide a secure, permanent URL re-direction service for Web applications. This service is run by the W3C Permanent Identifier Community Group. Web applications that deal with Linked Data often need to specify and use URLs that are very stable. They utilize services such as this one to ensure that applications using their URLs will always be re-directed to a working website. This website operates like a switchboard, connecting requests for information with the true location of the information on the Web. The switchboard can be reconfigured to point to a new location if the old location stops working.
W3ID | Permanent Identifiers for the Web

The Semantic Web for Earth and Environmental Terminology is a mature foundation ontology originally developed at the NASA Jet Propulsion Laboratory. Containing over 11000 concepts organized into ~200 ontologies, its top-level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), and Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). Since 2017, SWEET has been under the governance of the ESIP foundation.
SWEET | Semantic Web for Earth and Environmental Terminology

EnvO is a community ontology for the concise, controlled description of environments. ENVO helps humans, machines, and semantic web applications understand environmental entities of all kinds, from microscopic to intergalactic scales. As a FAIR-compliant resource, it promotes interoperability through the concise, controlled description of all things environmental.

Our federated metadata handling system relays the metadata PIDs (given to JSON-LD records) from our partners. The PID services used are diverse, including PURLs run by trusted and sustained organisations (e.g. OBO Foundry), DOIs, W3IDs, and IDs issued by trusted aggregators (e.g. OBIS). Not all metadata records integrated into our knowledge graph are assigned PIDs, a scenario we are gradually changing now that metadata records exist for use in Ocean InfoHub and ODIS.

Our federated metadata handling system relays the data-focused PIDs (given to the datasets described by our ODIS-Arch compliant JSON-LD records) from our partners. The PID services used are diverse, including PURLs run by trusted and sustained organisations (e.g. OBO Foundry), DOIs, W3IDs, and IDs issued by trusted aggregators (e.g. OBIS). We encourage the use of both human- and machine-friendly PIDs, or those with content negotiation enabled.

Members of our federation publish their own records as JSON-LD following the ODIS Arch specifications. These are harvested by Ocean InfoHub (for searchability and integration), but are also visible to all schema.org crawlers, including those from Google. Ocean InfoHub provides both a web front-end and a SPARQL endpoint for querying our knowledge graph.

The partners we federate use or maintain a wide range of services to publish the datasets they administer. Our knowledge graph technology does not republish the datasets, but links to the human-friendly distribution points (e.g. landing pages) and - where the partners provide it - the direct download distribution and its associated MIMEtype.

All exchanges use foundational web architecture and TCP/IP protocols, HTTP, HTTPS. Further details are provided here: https://book.oceaninfohub.org/content.html

TCP/IP family protocols, HTTP, HTTPS. Further details are provided here: https://book.oceaninfohub.org/content.html

Not Applicable - (meta)data shared do not require authorisation / authentication

Not Applicable as OIH does not store any data, but rather links to the locations of the data as hosted by providers.

We have the ability to preserve and version metadata shared by all partners in ODIS via our OIH indexer. We have not yet co-designed a policy with our stakeholders on the governance of this solution. There may be sensitivities on what should be archived and preserved for security, traditional/indigenous knowledge, conservation/protection, and other concerns.

Our federated stakeholders will all use schema.org and JSON Schema as lightweight KR languages. We provide guidance on how to embed more expressive KR languages in schema.org JSON-LD records, including the SKOS-level NERC vocabularies and OBO Foundry OWL ontologies. See more detaIls here: https://book.oceaninfohub.org/foundation/foundation.html

Not applicable as OIH does not handle data only metadata. NA - our solution is driven by metadata sharing. While access to datasets is provided (via links to the providers), we do not constrain what KR solutions stakeholders use on their data. Common semantics include the NERC vocabularies/SKOS resources and the Climate and Forecasting Variables, as well as environmentally-focused KR solutions from ESIP and OBO (GCMD, SWEET, ENVO).

Our federated stakeholders will all use schema.org and JSON Schema as lightweight KR languages. We provide guidance on how to embed more expressive KR languages in schema.org JSON-LD records, including the SKOS-level NERC vocabularies and OBO Foundry OWL ontologies.

Our solution is driven by metadata sharing. While access to datasets is provided (see responses F subprinciples), we do not constrain what KR solutions stakeholders use on their data. Common semantics include the NERC vocabularies/SKOS resources and the Climate and Forecasting Variables, as well as environmentally-focused KR solutions from ESIP and OBO (GCMD, SWEET, ENVO).

The terminology resources recommended do, themselves, follow the FAIR Principles to a high degree, with some exceptions.

We use schema.org serialised in JSON-LD, based on guidance from the Earth Science Information Partners' Science on Schema Cluster. We have expanded this with regularised patterns in the ODIS Architecture (ODIS-Arch) to increase consistency and actionability.

OIH does not constrain the semantic qualifications or data linking practices of our partners.

All metadata records are released openly on the web. The partners which share these may annotate them with license information, if they so wish

The partners in our federation are free to declare the license they release data under in the JSON-LD metadata documents they share with us and each other

schema.org fields which align closely to PROV-O. We inject a provenance block upon harvesting the metadata from our partners, to add to the chain of provenance. As the complexity of our digital ecosystem grows, we will consider separating the provenance graphs (which will also grow in size and complexity) and using PIDs to reference them. https://book.oceaninfohub.org/indexing/prov/

At this time, we do not constrain the provenance information of our partners datasets. However, stakeholders can express the provenance of their dataset in the JSON-LD documents they share using schema.org fields, which align well with PROV-O. https://book.oceaninfohub.org/indexing/prov/

AuScope Geochemistry Network (AGN) is an Australian consortium of Earth Science institutes cooperating to develop national geochemistry research infrastructure. The AGN was set up in 2019 in response to a national expression of need for better organisation and coordination of geochemistry laboratories and data.

How it works: Nanopublications linked to articles in RIO Journal

"How it works: Nanopublications linked to articles in RIO Journal"

This PARC Fair Data Policy (PFDP) defines the high level principles and conditions that govern provision, management, access, use and re-use of PARC data (both generated in projects and re-used from other sources), in line with the FAIR principles and the PARC Initial Data Management Plan (DMP) (D7.1), while taking into account legal aspects (i.e., GPDR), security, transparency, sustainability and quality of the data used and generated in PARC.

Metadata preservation policy: PFDP | PARC Fair Data Policy

Given a version number MAJOR.MINOR.PATCH, increment the: MAJOR version when you make incompatible API changes MINOR version when you add functionality in a backward compatible manner PATCH version when you make backward compatible bug fixes Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
SemVer | Semantic Versioning for software

FAIR-practice: SemVer | Semantic Versioning for software

Le Consortium de moyens mutualisés pour des services et données ouvertes en SHS (COMMONS), porté par OpenEdition, Métopes et Huma-Num, est l’un des projets lauréats de l’appel à manifestations d’intérêt Équipements structurants pour la recherche : EquipEx+ du Programme d’investissements d’avenir (PIA 3). Réunissant trois infrastructures françaises de premier plan dans le domaine des sciences humaines et sociales, COMMONS couvrira l’ensemble de la chaîne de production des connaissances, de la constitution des données à leur diffusion dans la sphère publique, contribuant ainsi à faire progresser la dynamique de la science ouverte.

HAL is a multidisciplinary open archive for the sharing of published and unpublished research. It is at the service of researchers in academic institutions, both public and private. In France, HAL is the national archive chosen by the scientific and academic community for the open dissemination of its research results. The repository is also at the service of researchers affiliated to foreign academic institutions, whether public or private.

HAL’s mission is to share and to archive scientific publications, of all disciplines, emanating from French or foreign research, public or private. Breaking with the enclosure of knowledge, HAL allows the free circulation of knowledge through rapid, transparent and complete dissemination of research results and open access to scientists as well as to the whole of civil society. By guaranteeing long-term access and preservation, HAL is also an open and sustainable instrument of scientific sovereignty.

Single Source Publishing XML-TEI set of tools.

Adults of the beetle species feed on feces of the Marmota bobak

Aphodius biguttatus (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Marmota (Marmota) bobak (Müller, 1776) (species)

Acrossus bimaculatus (Laxmann, 1770) (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Acrossus bimaculatus (Laxmann, 1770) (species)

Aphodius (Emadus) citellorum Semenov & Medvedev, 1929 (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius (Emadus) citellorum Semenov & Medvedev, 1929 (species)

Aphodius coenosus (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius distinctus (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius erraticus (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius (Aphodius) fimetarius (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius (Aphodius) fimetarius (species)

Aphodius granarius (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius haemorrhoidalis (Linnaeus, 1758) (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius haemorrhoidalis (Linnaeus, 1758) (species)

Aphodius immundus Creutzer, 1799 (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius immundus Creutzer, 1799 (species)

Aphodius luridus (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius melanostictus Schmidt, 1840 (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius melanostictus Schmidt, 1840 (species)

Aphodius prodromus (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius punctatosulcatus Sturm, 1805 (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius punctatosulcatus Sturm, 1805 (species)

Aphodius pusillus (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius quadriguttatus (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius quadrimaculatus (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)

Aphodius satellitius (species) - trophically interacts with - Marmota (Marmota) bobak (Müller, 1776) (species)