From e6109f688c4b74cc7f0b0cf8d5894068de408065 Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Thu, 24 Nov 2022 22:39:14 +0000 Subject: [PATCH] fixes issue #558 --- _ext/rdmkit_panel.py | 2 +- _static/faircookbook_rdmkit_mapping.yml | 124 ++++++++++++++++++ _static/recipes.json | 2 +- content/recipes/accessibility/aspera.md | 9 +- .../accessibility/aspera.md-figure1.svg | 1 + content/recipes/interoperability/nlp2kg.mmd | 19 +++ 6 files changed, 152 insertions(+), 5 deletions(-) create mode 100644 _static/faircookbook_rdmkit_mapping.yml create mode 100644 content/recipes/accessibility/aspera.md-figure1.svg create mode 100644 content/recipes/interoperability/nlp2kg.mmd diff --git a/_ext/rdmkit_panel.py b/_ext/rdmkit_panel.py index d4d13de7d..64833517d 100644 --- a/_ext/rdmkit_panel.py +++ b/_ext/rdmkit_panel.py @@ -53,7 +53,7 @@ def get_rdmkit_html(self): def parse_yaml(self): here_path = path.dirname(path.abspath(__file__)) - yaml_path = path.join(here_path, '..', '_static','faircookbook_rdmkit_mapping.yml') + yaml_path = path.join(here_path, '..', '_static', 'faircookbook_rdmkit_mapping.yml') json_path = path.join(here_path, '..', '_static', 'recipes.json') with open(yaml_path, 'r') as f: diff --git a/_static/faircookbook_rdmkit_mapping.yml b/_static/faircookbook_rdmkit_mapping.yml new file mode 100644 index 000000000..f6b4ac15f --- /dev/null +++ b/_static/faircookbook_rdmkit_mapping.yml @@ -0,0 +1,124 @@ +- rdmkit_title: Compliance monitoring & measurement + rdmkit_filename: compliance_monitoring + links: + - fcb_title: Creating a data/variable dictionary + fcb_id: FCB025 + - fcb_title: FAIR Evaluator tool + fcb_id: FCB049 + - fcb_title: FAIRshake tool + fcb_id: FCB050 + +- rdmkit_title: Data analysis + rdmkit_filename: data_analysis + links: + - fcb_title: Provenance information + fcb_id: FCB036 + +- rdmkit_title: Data organisation + rdmkit_filename: data_organisation + links: + - fcb_title: Creating a data/variable dictionary + fcb_id: FCB025 + - fcb_title: Creating a metadata profile + fcb_id: FCB026 + - fcb_title: Extraction, transformation, and loading process + fcb_id: FCB031 + +- rdmkit_title: Data protection + rdmkit_filename: data_protection + links: + - fcb_title: Data licenses + fcb_id: FCB034 + - fcb_title: Declaring data's permitted uses + fcb_id: FCB035 + +- rdmkit_title: Data publication + rdmkit_filename: data_publication + links: + - fcb_title: Depositing in Zenodo generic repository + fcb_id: FCB009 + +- rdmkit_title: Data quality + rdmkit_filename: data_quality + links: + - fcb_title: Provenance information + fcb_id: FCB036 + +- rdmkit_title: Data transfer + rdmkit_filename: data_transfer + links: + - fcb_title: Transferring data with SFTP + fcb_id: FCB014 + - fcb_title: Downloading data with Aspera + fcb_id: FCB015 + - fcb_title: Describe data by checksums + fcb_id: FCB052 + +- rdmkit_title: Identifiers + rdmkit_filename: identifiers + links: + - fcb_title: Unique, persistent identifiers + fcb_id: FCB006 + - fcb_title: InChI and SMILES identifiers for chemical structures + fcb_id: FCB007 + - fcb_title: Minting identifiers with Minid + fcb_id: FCB008 + +- rdmkit_title: Licensing + rdmkit_filename: licensing + links: + - fcb_title: Licensing + fcb_id: FCB032 + - fcb_title: Software licenses + fcb_id: FCB033 + - fcb_title: Data licenses + fcb_id: FCB034 + - fcb_title: Declaring data's permitted uses + fcb_id: FCB035 + +- rdmkit_title: Machine actionability + rdmkit_filename: machine_actionability + links: + - fcb_title: Unique, persistent identifiers + fcb_id: FCB006 + - fcb_title: Search engine optimization + fcb_id: FCB010 + - fcb_title: Creating a metadata profile + fcb_id: FCB026 + +- rdmkit_title: Documentation and metadata + rdmkit_filename: metadata_management + links: + - fcb_title: Introduction to terminologies and ontologies + fcb_id: FCB019 + - fcb_title: Creating data/variable dictionary + fcb_id: FCB025 + - fcb_title: Creating a metadata profile + fcb_id: FCB026 + - fcb_title: Search engine optimization + fcb_id: FCB010 + - fcb_title: Selecting terminologies and ontologies + fcb_id: FCB020 + - fcb_title: Requesting new terms + fcb_id: FCB021 + - fcb_title: Ontology-related tools and services + fcb_id: FCB022 + +- rdmkit_title: Sensitive data + rdmkit_filename: sensitive_data + links: + - fcb_title: Declaring data's permitted uses + fcb_id: FCB035 + +- rdmkit_title: Plant sciences + rdmkit_filename: plant_sciences + links: + - fcb_title: Plant genomic and genetic variation data submission to EMBL-EBI databases + fcb_id: FCB061 + +- rdmkit_title: Plant Genomics + rdmkit_filename: plant_genomics_assembly + links: + - fcb_title: Plant genomic and genetic variation data submission to EMBL-EBI databases + fcb_id: FCB061 + diff --git a/_static/recipes.json b/_static/recipes.json index 9e26dfeeb..d6b13c3a0 100644 --- a/_static/recipes.json +++ b/_static/recipes.json @@ -1 +1 @@ -{} \ No newline at end of file +{"Downloading data with Aspera protocol": {"name": "Downloading data with Aspera protocol", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB015", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB015"}, "Transferring data with SFTP protocol": {"name": "Transferring data with SFTP protocol", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB014", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB014"}, "Mapping datasets to CDISC-SDTM standard": {"name": "Mapping datasets to CDISC-SDTM standard", "reading_time": 20, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist", "Terminology Manager", "Ontologist"], "type": "Experience Report / Applied Example", "identifier": "FCB078", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB078"}, "Enhancing discoverability of EHDEN OHDSI data with Schema.org markup": {"name": "Enhancing discoverability of EHDEN OHDSI data with Schema.org markup", "reading_time": 15, "executable": "No", "audience": ["Terminology Manager", "Data Manager", "Data Scientist", "Ontologist"], "type": "Experience Report / Applied Example", "identifier": "FCB054", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB054"}, "eTox - omics datasets": {"name": "eTox - omics datasets", "reading_time": 20, "executable": "No", "audience": ["Data Manager", "Data Curator", "Ontologist"], "type": "Experience Report / Applied Example", "identifier": "FCB042", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB042"}, "Depositing High-Content Screening data to EBI BioImage Archive": {"name": "Depositing High-Content Screening data to EBI BioImage Archive", "reading_time": 15, "executable": "No", "audience": ["Data Manager"], "type": "Experience Report / Applied Example", "identifier": "FCB067", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB067"}, "Making an omics data matrix FAIR": {"name": "Making an omics data matrix FAIR", "reading_time": 30, "executable": "Yes", "audience": ["Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB037", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB037"}, "FAIRifying Data Matrices - Step1 - Starting material": {"name": "FAIRifying Data Matrices - Step1 - Starting material", "reading_time": 30, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB038", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB038"}, "FAIRifying Data Matrices - Step2 - Structuring data matrices": {"name": "FAIRifying Data Matrices - Step2 - Structuring data matrices", "reading_time": 30, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB039", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB039"}, "FAIRifying Data Matrices - Step3 - Exploring data with SPARQL": {"name": "FAIRifying Data Matrices - Step3 - Exploring data with SPARQL", "reading_time": 30, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB040", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB040"}, "FAIRifying Data Matrices - Step4 - Integrating data": {"name": "FAIRifying Data Matrices - Step4 - Integrating data", "reading_time": 30, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB041", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB041"}, "Making Computational Workflows FAIR": {"name": "Making Computational Workflows FAIR", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB062", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB062"}, "ND4BB - chemical activities datasets": {"name": "ND4BB - chemical activities datasets", "reading_time": 20, "executable": "No", "audience": ["Data Manager", "Data Curator"], "type": "Experience Report / Applied Example", "identifier": "FCB043", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB043"}, "Readying IMI Oncotrack - clinical cohort datasets for deposition to EBI Biosamples": {"name": "Readying IMI Oncotrack - clinical cohort datasets for deposition to EBI Biosamples", "reading_time": 10, "executable": "No", "audience": ["Data Manager", "Data Curator", "Ontologist"], "type": "Experience Report / Applied Example", "identifier": "FCB044", "maturity": "2", "url": "http://w3id.org/faircookbook/FCB044"}, "Depositing IMI ReSOLUTE transcriptomics datasets to EBI repositories": {"name": "Depositing IMI ReSOLUTE transcriptomics datasets to EBI repositories", "reading_time": 10, "executable": "No", "audience": ["Data Manager", "Data Curator", "Ontologist"], "type": "Experience Report / Applied Example", "identifier": "FCB045", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB045"}, "Assessing with FAIR Evaluator": {"name": "Assessing with FAIR Evaluator", "reading_time": 30, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB049", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB049"}, "Assessing with FAIRshake": {"name": "Assessing with FAIRshake", "reading_time": 30, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB050", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB050"}, "Creating file checksums": {"name": "Creating file checksums", "reading_time": 15, "executable": "No", "audience": ["Bioinformatician", "Data Scientist", "Data Engineer"], "type": "Hands-on", "identifier": "FCB052", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB052"}, "Validating checksums to verify file integrity": {"name": "Validating checksums to verify file integrity", "reading_time": 15, "executable": "No", "audience": ["Bioinformatician", "Data Scientist", "Data Engineer"], "type": "Hands-on", "identifier": "FCB053", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB053"}, "Introducing unique, persistent identifiers": {"name": "Introducing unique, persistent identifiers", "reading_time": 30, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Background information", "identifier": "FCB006", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB006"}, "Minting identifiers with Globus Minid client": {"name": "Minting identifiers with Globus Minid client", "reading_time": 10, "executable": "No", "audience": ["Software Developer", "Data Scientist"], "type": "Hands-on", "identifier": "FCB008", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB008"}, "Registering datasets with Wikidata": {"name": "Registering datasets with Wikidata", "reading_time": 15, "executable": "No", "audience": ["Bioinformatician", "Data Scientist", "Data Engineer"], "type": "Hands-on", "identifier": "FCB060", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB060"}, "Introducing Search Engine Optimization (SEO)": {"name": "Introducing Search Engine Optimization (SEO)", "reading_time": 10, "executable": "No", "audience": ["Software Developer", "Data Scientist"], "type": "Guidance", "identifier": "FCB010", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB010"}, "Marking up Data pages with Schema.org & Bioschemas for SEO": {"name": "Marking up Data pages with Schema.org & Bioschemas for SEO", "reading_time": 10, "executable": "No", "audience": ["Software Developer", "Data Scientist"], "type": "Guidance", "identifier": "FCB011", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB011"}, "Marking up Data Catalogue page with Schema.org & Bioschemas for SEO": {"name": "Marking up Data Catalogue page with Schema.org & Bioschemas for SEO", "reading_time": 10, "executable": "No", "audience": ["Software Developer", "Data Scientist"], "type": "Guidance", "identifier": "FCB013", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB013"}, "Marking up Dataset page with Schema.org & Bioschemas for SEO": {"name": "Marking up Dataset page with Schema.org & Bioschemas for SEO", "reading_time": 10, "executable": "No", "audience": ["Software Developer", "Data Scientist"], "type": "Guidance", "identifier": "FCB012", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB012"}, "Depositing to generic repositories - Zenodo use case": {"name": "Depositing to generic repositories - Zenodo use case", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist", "Funder"], "type": "Hands-on", "identifier": "FCB009", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB009"}, "Recipe Template": {"name": "Recipe Template", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist", "Funder"], "type": "Background information", "identifier": "FCB___", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB___"}, "Creating InChI & SMILES identifiers for chemical structures": {"name": "Creating InChI & SMILES identifiers for chemical structures", "reading_time": 15, "executable": "No", "audience": ["Chemoinformatician", "Data Curator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB007", "maturity": "4", "url": "https://w3id.org/faircookbook/FCB007"}, "Building a catalogue of datasets": {"name": "Building a catalogue of datasets", "reading_time": 60, "executable": "No", "audience": ["Data Manager", "Data Scientist", "Software Developer", "System Administrator"], "type": "Hands-on", "identifier": "FCB047", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB047"}, "Deploying a data catalogue - The IMI data catalogue example": {"name": "Deploying a data catalogue - The IMI data catalogue example", "reading_time": 20, "executable": "Yes", "audience": ["Software Developer", "Data Manager", "System Administrator"], "type": "Hands-on", "identifier": "FCB048", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB048"}, "Developing FAIR API for the Web": {"name": "Developing FAIR API for the Web", "reading_time": 30, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist", "Software Engineer"], "type": "Technical Guidance", "identifier": "FCB073", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB073"}, "Creating resolvable identifiers": {"name": "Creating resolvable identifiers", "reading_time": 30, "executable": "No", "audience": ["Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB077", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB077"}, "Introducing identifier resolution services": {"name": "Introducing identifier resolution services", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist", "Funder"], "type": "Background information", "identifier": "FCB046", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB046"}, "Creating InChIKeys for IUPAC names": {"name": "Creating InChIKeys for IUPAC names", "reading_time": 15, "executable": "Yes", "audience": ["Chemoinformatician", "Data Curator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB080", "maturity": "4", "url": "https://w3id.org/faircookbook/FCB080"}, "Using OpenRefine and Karma for FAIRification": {"name": "Using OpenRefine and Karma for FAIRification", "reading_time": 20, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Background information", "identifier": "FCB075", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB075"}, "Selecting an ontology lookup service": {"name": "Selecting an ontology lookup service", "reading_time": 20, "executable": "No", "audience": ["Data Manager", "Data Scientist", "Terminology Manager", "System Administrator", "Procurement Officer"], "type": "Survey / Review", "identifier": "FCB004", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB004"}, "Deploying EBI Ontology Lookup Service": {"name": "Deploying EBI Ontology Lookup Service", "reading_time": 20, "executable": "No", "audience": ["Data Manager", "Data Scientist", "Terminology Manager", "System Administrator"], "type": "Hands-on", "identifier": "FCB005", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB005"}, "Introducing vocabulary portals and lookup services": {"name": "Introducing vocabulary portals and lookup services", "reading_time": 20, "executable": "No", "audience": ["Data Manager", "Data Scientist", "Terminology Manager", "System Administrator"], "type": "Technical Guidance", "identifier": "FCB003", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB003"}, "Surveying extraction, transformation, load (ETL) tools": {"name": "Surveying extraction, transformation, load (ETL) tools", "reading_time": 15, "executable": "No", "audience": ["Data Curator", "Data Manager", "Data Scientist"], "type": "Survey / Review", "identifier": "FCB031", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB031"}, "Expressing Clinical Genetic Information as FHIR JSON": {"name": "Expressing Clinical Genetic Information as FHIR JSON", "reading_time": 15, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB058", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB058"}, "Outlining a metadata profile for Bioactivity data": {"name": "Outlining a metadata profile for Bioactivity data", "reading_time": 30, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB057", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB057"}, "Mapping identifiers with BridgeDb": {"name": "Mapping identifiers with BridgeDb", "reading_time": 30, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB017", "maturity": "4", "url": "https://w3id.org/faircookbook/FCB017"}, "Mapping identifiers using BridgeDb web services": {"name": "Mapping identifiers using BridgeDb web services", "reading_time": 30, "executable": "Yes", "audience": ["Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB018", "maturity": "4", "url": "https://w3id.org/faircookbook/FCB018"}, "Building a community compliant metadata profile - The Covid19 sample profile use case": {"name": "Building a community compliant metadata profile - The Covid19 sample profile use case", "reading_time": 30, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB028", "maturity": "4", "url": "https://w3id.org/faircookbook/FCB028"}, "Creating a data/variable dictionary": {"name": "Creating a data/variable dictionary", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Technical Guidance", "identifier": "FCB025", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB025"}, "Creating knowledge graphs from unstructured text": {"name": "Creating knowledge graphs from unstructured text", "reading_time": 45, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB081", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB081"}, "Creating a metadata profile": {"name": "Creating a metadata profile", "reading_time": 20, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB026", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB026"}, "Validating file format - FASTQ example": {"name": "Validating file format - FASTQ example", "reading_time": 15, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB030", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB030"}, "Converting from proprietary to open format": {"name": "Converting from proprietary to open format", "reading_time": 20, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB029", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB029"}, "Interlinking data from different sources": {"name": "Interlinking data from different sources", "reading_time": 30, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Background information", "identifier": "FCB016", "maturity": "4", "url": "https://w3id.org/faircookbook/FCB016"}, "Introducing terminologies and ontologies": {"name": "Introducing terminologies and ontologies", "reading_time": 15, "executable": "No", "audience": ["Data Curator", "Data Manager", "Data Scientist"], "type": "Survey / Review", "identifier": "FCB019", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB019"}, "Mapping Ontologies with OxO, EBI Ontology Xref Service": {"name": "Mapping Ontologies with OxO, EBI Ontology Xref Service", "reading_time": 30, "executable": "No", "audience": ["Ontologist", "Terminology Manager", "Data Scientist", "Data Curator", "Data Manager"], "type": "Hands-on", "identifier": "FCB076", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB076"}, "Requesting new terms from terminologies and ontologies": {"name": "Requesting new terms from terminologies and ontologies", "reading_time": 15, "executable": "No", "audience": ["Terminology Manager", "Data Manager", "Data Scientist", "Ontologist"], "type": "Guidance", "identifier": "FCB021", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB021"}, "Introducing ontology-related tools and services": {"name": "Introducing ontology-related tools and services", "reading_time": 15, "executable": "No", "audience": ["Data Curator", "Data Manager", "Data Scientist", "Ontologist", "Software Engineer", "Terminology Manager"], "type": "Survey / Review", "identifier": "FCB022", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB022"}, "Building an application ontology with ROBOT": {"name": "Building an application ontology with ROBOT", "reading_time": 60, "executable": "Yes", "audience": ["Terminology Manager", "Data Manager", "Data Scientist", "Ontologist"], "type": "Hands-on", "identifier": "FCB023", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB023"}, "Building an application ontology for metabolomics - MSIO": {"name": "Building an application ontology for metabolomics - MSIO", "reading_time": 30, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB024", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB024"}, "Inventorying tools for converting data to RDF": {"name": "Inventorying tools for converting data to RDF", "reading_time": 30, "executable": "No", "audience": ["Data Producer", "Data Engineer"], "type": "Inventory", "identifier": "FCB051", "maturity": "4", "url": "https://w3id.org/faircookbook/FCB051"}, "Selecting terminologies and ontologies": {"name": "Selecting terminologies and ontologies", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Terminology Manager", "Data Scientist", "Ontologist"], "type": "Guidance", "identifier": "FCB020", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB020"}, "Outlining a metadata profile for transcriptomics": {"name": "Outlining a metadata profile for transcriptomics", "reading_time": 30, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Terminology Manager", "Data Scientist", "Ontologist"], "type": "Guidance", "identifier": "FCB027", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB027"}, "Converting VCF file to FHIR JSON": {"name": "Converting VCF file to FHIR JSON", "reading_time": 30, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB059", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB059"}, "Understanding the relation between FAIR and Knowledge Graphs": {"name": "Understanding the relation between FAIR and Knowledge Graphs", "reading_time": 10, "executable": "No", "audience": ["Everyone"], "type": "Guidance", "identifier": "FCB070", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB070"}, "Reflecting on the ethical values of FAIR": {"name": "Reflecting on the ethical values of FAIR", "reading_time": 15, "executable": "No", "audience": ["Everyone"], "type": "Perspective", "identifier": "FCB072", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB072"}, "Practical Considerations for CROs to play FAIR": {"name": "Practical Considerations for CROs to play FAIR", "reading_time": 15, "executable": "No", "audience": ["Procurement Officer", "Principal Investigator", "Data Curator", "Data Manager", "Data Scientist"], "type": "Background information", "identifier": "FCB056", "maturity": "2", "url": "http://w3id.org/faircookbook/FCB056"}, "Introducing our FAIRification framework": {"name": "Introducing our FAIRification framework", "reading_time": 20, "executable": "No", "audience": ["Everyone"], "type": "Experience Report / Applied Example", "identifier": "FCB079", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB079"}, "Framing FAIR and the notion of metadata": {"name": "Framing FAIR and the notion of metadata", "reading_time": 10, "executable": "No", "audience": ["Everyone"], "type": "Guidance", "identifier": "FCB068", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB068"}, "Prioritizing projects for FAIRification": {"name": "Prioritizing projects for FAIRification", "reading_time": 10, "executable": "No", "audience": ["Everyone"], "type": "Guidance", "identifier": "FCB055", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB055"}, "Raising Awareness in Public Knowledge Graphs for Life Sciences": {"name": "Raising Awareness in Public Knowledge Graphs for Life Sciences", "reading_time": 10, "executable": "No", "audience": ["Everyone"], "type": "Guidance", "identifier": "FCB071", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB071"}, "Training for FAIRification with open or synthetic biomedical datasets": {"name": "Training for FAIRification with open or synthetic biomedical datasets", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Terminology Manager", "Data Scientist"], "type": "Guidance", "identifier": "FCB069", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB069"}, "Minimal Data Maturity with ISA - ISA-Tab and free text": {"name": "Minimal Data Maturity with ISA - ISA-Tab and free text", "reading_time": 15, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB063", "maturity": "1", "url": "https://w3id.org/faircookbook/FCB063"}, "Enhanced Data Maturity with ISA - ISA-JSON and ontology markup": {"name": "Enhanced Data Maturity with ISA - ISA-JSON and ontology markup", "reading_time": 15, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB064", "maturity": "2", "url": "https://w3id.org/faircookbook/FCB064"}, "Dissemination - Packaging ISA as a Research Object (RO)": {"name": "Dissemination - Packaging ISA as a Research Object (RO)", "reading_time": 15, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB066", "maturity": "4", "url": "https://w3id.org/faircookbook/FCB066"}, "Moving to a semantically typed version - ISA-JSON-LD": {"name": "Moving to a semantically typed version - ISA-JSON-LD", "reading_time": 15, "executable": "Yes", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Hands-on", "identifier": "FCB065", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB065"}, "Licensing": {"name": "Licensing", "reading_time": 15, "executable": "No", "audience": ["Everyone"], "type": "Guidance", "identifier": "FCB032", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB032"}, "Licensing Data": {"name": "Licensing Data", "reading_time": 15, "executable": "No", "audience": ["Everyone"], "type": "Guidance", "identifier": "FCB034", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB034"}, "Licensing Software": {"name": "Licensing Software", "reading_time": 15, "executable": "No", "audience": ["Everyone"], "type": "Guidance", "identifier": "FCB033", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB033"}, "Declaring data permitted uses": {"name": "Declaring data permitted uses", "reading_time": 15, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist", "Ontologist"], "type": "Background information", "identifier": "FCB035", "maturity": "4", "url": "https://w3id.org/faircookbook/FCB035"}, "Improving dataset maturity - the MIAPPE use case": {"name": "Improving dataset maturity - the MIAPPE use case", "reading_time": 30, "executable": "No", "audience": ["Everyone"], "type": "Guidance", "identifier": "FCB061", "maturity": "3", "url": "https://w3id.org/faircookbook/FCB061"}, "Introducing Provenance Information": {"name": "Introducing Provenance Information", "reading_time": 20, "executable": "No", "audience": ["Principal Investigator", "Data Manager", "Data Scientist"], "type": "Background information", "identifier": "FCB036", "maturity": "0", "url": "https://w3id.org/faircookbook/FCB036"}} \ No newline at end of file diff --git a/content/recipes/accessibility/aspera.md b/content/recipes/accessibility/aspera.md index ee48f40b9..86862cf15 100644 --- a/content/recipes/accessibility/aspera.md +++ b/content/recipes/accessibility/aspera.md @@ -25,14 +25,17 @@ This recipe covers documentation of the popular Aspera Fast Transfer Protocol an ````{dropdown} :open: -```{figure} aspera.md-figure1.mmd +```{figure} aspera.md-figure1.svg +--- width: 650px name: aspera-figure1 -subtitle: Aspera Data Transfer Process. +alt: Aspera Data Transfer Process. +--- +Aspera Data Transfer Process. ``` ```` ---- + ## Obtain Aspera services ### Get accounts permissions diff --git a/content/recipes/accessibility/aspera.md-figure1.svg b/content/recipes/accessibility/aspera.md-figure1.svg new file mode 100644 index 000000000..5be54e234 --- /dev/null +++ b/content/recipes/accessibility/aspera.md-figure1.svg @@ -0,0 +1 @@ +
Yes
No
Yes
No
Data on source repository, with aspera as a transfer option
Do you have an account
on source repository?
Install aspera software, and
work out the appropriate command line options
Obtain access credentials on source repository
Does your system have
the applicable firewall holes?
Start download
Get firewall holes from IT department
Download finished
 \ No newline at end of file diff --git a/content/recipes/interoperability/nlp2kg.mmd b/content/recipes/interoperability/nlp2kg.mmd new file mode 100644 index 000000000..971313430 --- /dev/null +++ b/content/recipes/interoperability/nlp2kg.mmd @@ -0,0 +1,19 @@ +graph TD; + + A(fa:fa-search Literature search):::box2 -->|is a| B(fa:fa-book fa:fa-file-alt text corpus):::box2 + + B --> |Named Entity Recognition - Term tagging|C(fa:fa-tags tagged text):::box2 + + C --> |Coreference-based disambiguation |D( fa:fa-circle-check disambiguated & fa:fa-tags tagged text):::box2 + + D --> |Relation detection| E(fa:fa-tags entity fa:fa-tags relation tagged text):::box2 + + E --> |predicate extraction| F(fas:fa-diagram-project RDF linked data graph):::box + + F --> |persistence to an RDF triple store| G(fa:fa-database SPARQL endpoint):::box2 + +classDef box font-family:avenir,font-size:14px,fill:#B30000,stroke:#222,color:#fff,stroke-width:1px +classDef box2 font-family:avenir,font-size:14px,fill:orange,stroke:#222,color:#fff,stroke-width:1px + +linkStyle 0,1,2,3,4,5 stroke:#B30000,stroke-width:1px,color:#B30000,font-family:avenir,font-size:10px +linkStyle 5 stroke:#B30000,font-family:avenir,stroke-width:1px,color:#B30000,stroke-dasharray:5 \ No newline at end of file