From fae28d09ac7f0b28d204d4c5728697c3254ea090 Mon Sep 17 00:00:00 2001 From: ginger Date: Mon, 1 May 2023 10:00:52 -0700 Subject: [PATCH 01/40] update taxon/taxonname types since autogenerator does not work with types --- _data/type_versions.yaml | 8 +- pages/_types/Taxon/1.0-RELEASE.html | 269 ++++++++ pages/_types/TaxonName/1.0-RELEASE.html | 807 ++++++++++++++++++++++++ 3 files changed, 1080 insertions(+), 4 deletions(-) create mode 100644 pages/_types/Taxon/1.0-RELEASE.html create mode 100644 pages/_types/TaxonName/1.0-RELEASE.html diff --git a/_data/type_versions.yaml b/_data/type_versions.yaml index dc3d3384e..a37901adb 100644 --- a/_data/type_versions.yaml +++ b/_data/type_versions.yaml @@ -123,14 +123,14 @@ Study: Taxon: name: "Taxon" - latest_publication: "0.4-DRAFT" - latest_release: "0.3-RELEASE-2019_11_18" + latest_publication: "1.0-RELEASE" + latest_release: "1.0-RELEASE" status: "active" TaxonName: name: "TaxonName" - latest_publication: "0.1-DRAFT" - latest_release: + latest_publication: "1.0-RELEASE" + latest_release: "1.0-RELEASE" status: "active" --- diff --git a/pages/_types/Taxon/1.0-RELEASE.html b/pages/_types/Taxon/1.0-RELEASE.html new file mode 100644 index 000000000..42a99d8e1 --- /dev/null +++ b/pages/_types/Taxon/1.0-RELEASE.html @@ -0,0 +1,269 @@ +--- +redirect_from: +- "/types/Taxon/" +- "/types/Taxon" + +previous_version: '0.4-DRAFT' +previous_release: '0.3-RELEASE-2019_11_18' + + +dateModified: 2023-05-01 +description: "A set of organisms asserted to represent a natural cohesive biological unit." +hierarchy: +- Thing +gh_tasks: https://github.com/Bioschemas/specifications/labels/type%3A%20Taxon +group: biodiversity +name: Taxon +parent_type: Thing +spec_type: Type +status: revision #Revert to revision when working on the next version +version: '1.0-RELEASE' +--- + +{% include type-start.html %} + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
PropertyExpected TypeDescription
Properties from Taxon
+ + alternateScientificName + + TaxonName  or
+ Text  or
+ URL  + + 		A TaxonName representing a scientific name, with authorship and date information if known, of a synonym of the currently valid (zoological) or accepted (botanical) name.
+ + childTaxon + + Taxon  or
+ Text  or
+ URL  + + 		Closest child taxa of the taxon in question.
Inverse property: parentTaxon.
+ + parentTaxon + + Taxon  or
+ Text  or
+ URL  + + 		Closest parent taxon of the taxon in question.
Inverse property: childTaxon.
+ + scientificName + + TaxonName  or
+ Text  or
+ URL  + + 		A TaxonName representing the currently valid (zoological) or accepted (botanical) name for that taxon.
+ + taxonRank + + PropertyValue  or
+ Text  or
+ URL  + + + 		The taxonomic rank of this taxon given preferably as a URI from a controlled vocabulary – (typically the ranks from TDWG TaxonRank ontology or equivalent Wikidata URIs).
Properties from Thing
+ + additionalType + + URL  + + An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.
+ + alternateName + + Text  + + An alias for the item.
+ + description + + Text  + + A description of the item.
+ + disambiguatingDescription + + Text  + + A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.
+ + identifier + + PropertyValue  or
+ Text  or
+ URL  + + 		The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.
+ + image + + ImageObject  or
+ URL  + + 		An image of the item. This can be a URL or a fully described ImageObject.
+ + mainEntityOfPage + + CreativeWork  or
+ URL  + + 		Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.
Inverse property: mainEntity.
+ + name + + Text  + + The name of the item.
+ + potentialAction + + Action  + + Indicates a potential Action, which describes an idealized action in which this thing would play an 'object' role.
+ + sameAs + + URL  + + URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.
+ + subjectOf + + CreativeWork  or
+ Event  + + 		A CreativeWork or Event about this Thing.
Inverse property: about.
+ + url + + URL  + + URL of the item.
+
diff --git a/pages/_types/TaxonName/1.0-RELEASE.html b/pages/_types/TaxonName/1.0-RELEASE.html new file mode 100644 index 000000000..ee66a9046 --- /dev/null +++ b/pages/_types/TaxonName/1.0-RELEASE.html @@ -0,0 +1,807 @@ +--- +redirect_from: +- "/types/TaxonName" +- "/types/TaxonName/" + +previous_version: '0.1-DRAFT' +previous_release: + + +dateModified: 2023-05-01 +description: A name of a biological taxon, may it be valid (zoology) / accepted (botany) or not +hierarchy: +- Thing +- CreativeWork +gh_tasks: https://github.com/Bioschemas/specifications/labels/type%3A%20Taxon +group: biodiversity +name: TaxonName +parent_type: CreativeWork +spec_type: Type +status: revision #Revert to revision when working on the next version +version: '1.0-RELEASE' +--- + + +{% include type-start.html %} +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
PropertyExpected TypeDescription
Properties from TaxonName
+ +taxonRank + +PropertyValue  or
Text  or
URL 		The taxonomic rank of this taxon given preferably as a URI from a controlled vocabulary – (typically the ranks from TDWG TaxonRank ontology or equivalent Wikidata URIs).
Properties from CreativeWork
+ +about + +Thing The subject matter of the content.
Inverse property: subjectOf.
+ +accessMode + +Text The human sensory perceptual system or cognitive faculty through which a person may process or perceive information. Expected values include: auditory, tactile, textual, visual, colorDependent, chartOnVisual, chemOnVisual, diagramOnVisual, mathOnVisual, musicOnVisual, textOnVisual.
+ +accessModeSufficient + +ItemList A list of single or combined accessModes that are sufficient to understand all the intellectual content of a resource. Expected values include: auditory, tactile, textual, visual.
+ +accessibilityAPI + +Text Indicates that the resource is compatible with the referenced accessibility API (WebSchemas wiki lists possible values).
+ +accessibilityControl + +Text Identifies input methods that are sufficient to fully control the described resource (WebSchemas wiki lists possible values).
+ +accessibilityFeature + +Text Content features of the resource, such as accessible media, alternatives and supported enhancements for accessibility (WebSchemas wiki lists possible values).
+ +accessibilityHazard + +Text A characteristic of the described resource that is physiologically dangerous to some users. Related to WCAG 2.0 guideline 2.3 (WebSchemas wiki lists possible values).
+ +accessibilitySummary + +Text A human-readable summary of specific accessibility features or deficiencies, consistent with the other accessibility metadata but expressing subtleties such as "short descriptions are present but long descriptions will be needed for non-visual users" or "short descriptions are present and no long descriptions are needed."
+ +accountablePerson + +Person Specifies the Person that is legally accountable for the CreativeWork.
+ +aggregateRating + +AggregateRating The overall rating, based on a collection of reviews or ratings, of the item.
+ +alternativeHeadline + +Text A secondary title of the CreativeWork.
+ +associatedMedia + +MediaObject A media object that encodes this CreativeWork. This property is a synonym for encoding.
+ +audience + +Audience An intended audience, i.e. a group for whom something was created. Supersedes serviceAudience.
+ +audio + +AudioObject  or
Clip 		An embedded audio object.
+ +author + +Organization  or
Person 		The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.
+ +award + +Text An award won by or for this item. Supersedes awards.
+ +character + +Person Fictional person connected with a creative work.
+ +citation + +CreativeWork  or
Text 		A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.
+ +comment + +Comment Comments, typically from users.
+ +commentCount + +Integer The number of comments this CreativeWork (e.g. Article, Question or Answer) has received. This is most applicable to works published in Web sites with commenting system; additional comments may exist elsewhere.
+ +conditionsOfAccess + +Text Conditions that affect the availability of, or method(s) of access to, an item. Typically used for real world items such as an ArchiveComponent held by an ArchiveOrganization. This property is not suitable for use as a general Web access control mechanism. It is expressed only in natural language.

+ +For example "Available by appointment from the Reading Room" or "Accessible only from logged-in accounts ".
+ +contentLocation + +Place The location depicted or described in the content. For example, the location in a photograph or painting.
+ +contentRating + +Rating  or
Text 		Official rating of a piece of content—for example,'MPAA PG-13'.
+ +contentReferenceTime + +DateTime The specific time described by a creative work, for works (e.g. articles, video objects etc.) that emphasise a particular moment within an Event.
+ +contributor + +Organization  or
Person 		A secondary contributor to the CreativeWork or Event.
+ +copyrightHolder + +Organization  or
Person 		The party holding the legal copyright to the CreativeWork.
+ +copyrightYear + +Number The year during which the claimed copyright for the CreativeWork was first asserted.
+ +correction + +CorrectionComment  or
Text  or
URL 		Indicates a correction to a CreativeWork, either via a CorrectionComment, textually or in another document.
+ +creativeWorkStatus + +DefinedTerm  or
Text 		The status of a creative work in terms of its stage in a lifecycle. Example terms include Incomplete, Draft, Published, Obsolete. Some organizations define a set of terms for the stages of their publication lifecycle.
+ +creator + +Organization  or
Person 		The creator/author of this CreativeWork. This is the same as the Author property for CreativeWork.
+ +dateCreated + +Date  or
DateTime 		The date on which the CreativeWork was created or the item was added to a DataFeed.
+ +dateModified + +Date  or
DateTime 		The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.
+ +datePublished + +Date Date of first broadcast/publication.
+ +discussionUrl + +URL A link to the page containing the comments of the CreativeWork.
+ +editor + +Person Specifies the Person who edited the CreativeWork.
+ +educationalAlignment + +AlignmentObject An alignment to an established educational framework.
+ +educationalUse + +Text The purpose of a work in the context of education; for example, 'assignment', 'group work'.
+ +encoding + +MediaObject A media object that encodes this CreativeWork. This property is a synonym for associatedMedia. Supersedes encodings.
Inverse property: encodesCreativeWork.
+ +encodingFormat + +Text  or
URL 		Media type typically expressed using a MIME format (see IANA site and MDN reference) e.g. application/zip for a SoftwareApplication binary, audio/mpeg for .mp3 etc.).

+ +In cases where a CreativeWork has several media type representations, encoding can be used to indicate each MediaObject alongside particular encodingFormat information.

+ +Unregistered or niche encoding and file formats can be indicated instead via the most appropriate URL, e.g. defining Web page or a Wikipedia/Wikidata entry. Supersedes fileFormat.
+ +exampleOfWork + +CreativeWork A creative work that this work is an example/instance/realization/derivation of.
Inverse property: workExample.
+ +expires + +Date Date the content expires and is no longer useful or available. For example a VideoObject or NewsArticle whose availability or relevance is time-limited, or a ClaimReview fact check whose publisher wants to indicate that it may no longer be relevant (or helpful to highlight) after some date.
+ +funder + +Organization  or
Person 		A person or organization that supports (sponsors) something through some kind of financial contribution.
+ +genre + +Text  or
URL 		Genre of the creative work, broadcast channel or group.
+ +hasPart + +CreativeWork Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense).
Inverse property: isPartOf.
+ +headline + +Text Headline of the article.
+ +inLanguage + +Language  or
Text 		The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also availableLanguage. Supersedes language.
+ +interactionStatistic + +InteractionCounter The number of interactions for the CreativeWork using the WebSite or SoftwareApplication. The most specific child type of InteractionCounter should be used. Supersedes interactionCount.
+ +interactivityType + +Text The predominant mode of learning supported by the learning resource. Acceptable values are 'active', 'expositive', or 'mixed'.
+ +isAccessibleForFree + +Boolean A flag to signal that the item, event, or place is accessible for free. Supersedes free.
+ +isBasedOn + +CreativeWork  or
Product  or
URL 		A resource from which this work is derived or from which it is a modification or adaption. Supersedes isBasedOnUrl.
+ +isBasisFor + +CreativeWork A resource that was (somehow) created using this resource as a basis for.
Inverse property: isBasedOn.
+ +isFamilyFriendly + +Boolean Indicates whether this content is family friendly.
+ +isPartOf + +CreativeWork Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.
Inverse property: hasPart.
+ +keywords + +Text Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.
+ +learningResourceType + +Text The predominant type or kind characterizing the learning resource. For example, 'presentation', 'handout'.
+ +license + +CreativeWork  or
URL 		A license document that applies to this content, typically indicated by URL.
+ +locationCreated + +Place The location where the CreativeWork was created, which may not be the same as the location depicted in the CreativeWork.
+ +mainEntity + +Thing Indicates the primary entity described in some page or other CreativeWork.
Inverse property: mainEntityOfPage.
+ +material + +Product  or
Text  or
URL 		A material that something is made from, e.g. leather, wool, cotton, paper.
+ +materialExtent + +QuantitativeValue  or
Text 		The quantity of the materials being described or an expression of the physical space they occupy.
+ +mentions + +Thing Indicates that the CreativeWork contains a reference to, but is not necessarily about a concept.
+ +offers + +Offer An offer to provide this item—for example, an offer to sell a product, rent the DVD of a movie, perform a service, or give away tickets to an event.
+ +position + +Integer  or
Text 		The position of an item in a series or sequence of items.
+ +producer + +Organization  or
Person 		The person or organization who produced the work (e.g. music album, movie, tv/radio series etc.).
+ +provider + +Organization  or
Person 		The service provider, service operator, or service performer; the goods producer. Another party (a seller) may offer those services or goods on behalf of the provider. A provider may also serve as the seller. Supersedes carrier.
+ +publication + +PublicationEvent A publication event associated with the item.
+ +publisher + +Organization  or
Person 		The publisher of the creative work.
+ +publisherImprint + +Organization The publishing division which published the comic.
+ +publishingPrinciples + +CreativeWork  or
URL 		The publishingPrinciples property indicates (typically via URL) a document describing the editorial principles of an Organization (or individual e.g. a Person writing a blog) that relate to their activities as a publisher, e.g. ethics or diversity policies. When applied to a CreativeWork (e.g. NewsArticle) the principles are those of the party primarily responsible for the creation of the CreativeWork.

+ +While such policies are most typically expressed in natural language, sometimes related information (e.g. indicating a funder) can be expressed using schema.org terminology.
+ +recordedAt + +Event The Event where the CreativeWork was recorded. The CreativeWork may capture all or part of the event.
Inverse property: recordedIn.
+ +releasedEvent + +PublicationEvent The place and time the release was issued, expressed as a PublicationEvent.
+ +review + +Review A review of the item. Supersedes reviews.
+ +schemaVersion + +Text  or
URL 		Indicates (by URL or string) a particular version of a schema used in some CreativeWork. For example, a document could declare a schemaVersion using an URL such as http://schema.org/version/2.0/ if precise indication of schema version was required by some application.
+ +sdDatePublished + +Date Indicates the date on which the current structured data was generated / published. Typically used alongside sdPublisher
+ +sdLicense + +CreativeWork  or
URL 		A license document that applies to this structured data, typically indicated by URL.
+ +sdPublisher + +Organization  or
Person 		Indicates the party responsible for generating and publishing the current structured data markup, typically in cases where the structured data is derived automatically from existing published content but published on a different site. For example, student projects and open data initiatives often re-publish existing content with more explicitly structured metadata. The +sdPublisher property helps make such practices more explicit.
+ +sourceOrganization + +Organization The Organization on whose behalf the creator was working.
+ +spatial + +Place The "spatial" property can be used in cases when more specific properties +(e.g. locationCreated, spatialCoverage, contentLocation) are not known to be appropriate.
+ +spatialCoverage + +Place The spatialCoverage of a CreativeWork indicates the place(s) which are the focus of the content. It is a subproperty of +contentLocation intended primarily for more technical and detailed materials. For example with a Dataset, it indicates +areas that the dataset describes: a dataset of New York weather would have spatialCoverage which was the place: the state of New York.
+ +sponsor + +Organization  or
Person 		A person or organization that supports a thing through a pledge, promise, or financial contribution. e.g. a sponsor of a Medical Study or a corporate sponsor of an event.
+ +temporal + +DateTime  or
Text 		The "temporal" property can be used in cases where more specific properties +(e.g. temporalCoverage, dateCreated, dateModified, datePublished) are not known to be appropriate.
+ +temporalCoverage + +DateTime  or
Text  or
URL 		The temporalCoverage of a CreativeWork indicates the period that the content applies to, i.e. that it describes, either as a DateTime or as a textual string indicating a time period in ISO 8601 time interval format. In +the case of a Dataset it will typically indicate the relevant time period in a precise notation (e.g. for a 2011 census dataset, the year 2011 would be written "2011/2012"). Other forms of content e.g. ScholarlyArticle, Book, TVSeries or TVEpisode may indicate their temporalCoverage in broader terms - textually or via well-known URL. +Written works such as books may sometimes have precise temporal coverage too, e.g. a work set in 1939 - 1945 can be indicated in ISO 8601 interval format format via "1939/1945".

+ +Open-ended date ranges can be written with ".." in place of the end date. For example, "2015-11/.." indicates a range beginning in November 2015 and with no specified final date. This is tentative and might be updated in future when ISO 8601 is officially updated. Supersedes datasetTimeInterval.
+ +text + +Text The textual content of this CreativeWork.
+ +thumbnailUrl + +URL A thumbnail image relevant to the Thing.
+ +timeRequired + +Duration Approximate or typical time it takes to work with or through this learning resource for the typical intended target audience, e.g. 'PT30M', 'PT1H25M'.
+ +translationOfWork + +CreativeWork The work that this work has been translated from. e.g. 物种起源 is a translationOf “On the Origin of Species”
Inverse property: workTranslation.
+ +translator + +Organization  or
Person 		Organization or person who adapts a creative work to different languages, regional differences and technical requirements of a target market, or that translates during some event.
+ +typicalAgeRange + +Text The typical expected age range, e.g. '7-9', '11-'.
+ +version + +Number  or
Text 		The version of the CreativeWork embodied by a specified resource.
+ +video + +Clip  or
VideoObject 		An embedded video object.
+ +workExample + +CreativeWork Example/instance/realization/derivation of the concept of this creative work. eg. The paperback edition, first edition, or eBook.
Inverse property: exampleOfWork.
+ +workTranslation + +CreativeWork A work that is a translation of the content of this work. e.g. 西遊記 has an English workTranslation “Journey to the West”,a German workTranslation “Monkeys Pilgerfahrt” and a Vietnamese translation Tây du ký bình khảo.
Inverse property: translationOfWork.
Properties from Thing
+ +additionalType + +URL An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.
+ +alternateName + +Text An alias for the item.
+ +description + +Text A description of the item.
+ +disambiguatingDescription + +Text A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.
+ +identifier + +PropertyValue  or
Text  or
URL 		The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.
+ +image + +ImageObject  or
URL 		An image of the item. This can be a URL or a fully described ImageObject.
+ +mainEntityOfPage + +CreativeWork  or
URL 		Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.
Inverse property: mainEntity.
+ +name + +Text The name of the item.
+ +potentialAction + +Action Indicates a potential Action, which describes an idealized action in which this thing would play an 'object' role.
+ +sameAs + +URL URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.
+ +subjectOf + +CreativeWork  or
Event 		A CreativeWork or Event about this Thing.
Inverse property: about.
+ +url + +URL URL of the item.
+
+ From 8b2d8b7a74756d23fcd786b14468b7dddaf74d87 Mon Sep 17 00:00:00 2001 From: ginger Date: Mon, 1 May 2023 10:25:24 -0700 Subject: [PATCH 02/40] fix tag for release vs revision --- pages/_types/Taxon/1.0-RELEASE.html | 2 +- pages/_types/TaxonName/1.0-RELEASE.html | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/_types/Taxon/1.0-RELEASE.html b/pages/_types/Taxon/1.0-RELEASE.html index 42a99d8e1..2785165be 100644 --- a/pages/_types/Taxon/1.0-RELEASE.html +++ b/pages/_types/Taxon/1.0-RELEASE.html @@ -16,7 +16,7 @@ name: Taxon parent_type: Thing spec_type: Type -status: revision #Revert to revision when working on the next version +status: release #Revert to revision when working on the next version version: '1.0-RELEASE' --- diff --git a/pages/_types/TaxonName/1.0-RELEASE.html b/pages/_types/TaxonName/1.0-RELEASE.html index ee66a9046..1ba9d82ad 100644 --- a/pages/_types/TaxonName/1.0-RELEASE.html +++ b/pages/_types/TaxonName/1.0-RELEASE.html @@ -17,7 +17,7 @@ name: TaxonName parent_type: CreativeWork spec_type: Type -status: revision #Revert to revision when working on the next version +status: release #Revert to revision when working on the next version version: '1.0-RELEASE' --- From 0bd52f2d31104fb7554b936d8b6ff11be0209597 Mon Sep 17 00:00:00 2001 From: ginger Date: Mon, 1 May 2023 10:41:49 -0700 Subject: [PATCH 03/40] add missing dwc:vernacularName --- pages/_types/Taxon/1.0-RELEASE.html | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/pages/_types/Taxon/1.0-RELEASE.html b/pages/_types/Taxon/1.0-RELEASE.html index 2785165be..0f7d7e19e 100644 --- a/pages/_types/Taxon/1.0-RELEASE.html +++ b/pages/_types/Taxon/1.0-RELEASE.html @@ -265,5 +265,24 @@ URL of the item. + + Properties from Darwin Core + + + + + + + + + dwc:vernacularName + + + Text  + + + A vernacular (common) name of the taxon. + + From 7203dd317767306c77eada73f2766211c1e597cc Mon Sep 17 00:00:00 2001 From: gtsueng Date: Mon, 22 May 2023 09:36:47 -0700 Subject: [PATCH 04/40] Update type_versions.yaml fix issue of latest draft being a release --- _data/type_versions.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_data/type_versions.yaml b/_data/type_versions.yaml index a37901adb..b5c09ecfa 100644 --- a/_data/type_versions.yaml +++ b/_data/type_versions.yaml @@ -123,13 +123,13 @@ Study: Taxon: name: "Taxon" - latest_publication: "1.0-RELEASE" + latest_publication: "0.4-DRAFT" latest_release: "1.0-RELEASE" status: "active" TaxonName: name: "TaxonName" - latest_publication: "1.0-RELEASE" + latest_publication: "0.1-DRAFT" latest_release: "1.0-RELEASE" status: "active" From 1b7a6b9a0e0b97d01a772cf919681caebbf7d03d Mon Sep 17 00:00:00 2001 From: David Fichtmueller Date: Tue, 30 May 2023 15:53:16 +0200 Subject: [PATCH 05/40] fixed error in example for alternateName: wrong quotation mark --- pages/_profiles/Dataset/1.0-RELEASE.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/_profiles/Dataset/1.0-RELEASE.html b/pages/_profiles/Dataset/1.0-RELEASE.html index 58f39088d..3c03ac465 100644 --- a/pages/_profiles/Dataset/1.0-RELEASE.html +++ b/pages/_profiles/Dataset/1.0-RELEASE.html @@ -49,7 +49,7 @@ "alternateName": "MetaboLights dataset", "alternateName": "Automated Label-free Quantification of Metabolites from Liquid Chromatography", "alternateName": "Mass Spectrometry Data (Plasma) Automated Label-free Quantification of Metabolites from Liquid Chromatography", - "alternateName": “Mass Spectrometry Data (Plasma)" + "alternateName": "Mass Spectrometry Data (Plasma)" } - property: citation expected_types: From 097605d284657df226ccc0b4a3c648027deaa12a Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Tue, 6 Jun 2023 23:09:52 +1200 Subject: [PATCH 06/40] feat: add MetabolicAtlas as a live deploy --- _data/live_deployments.json | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/_data/live_deployments.json b/_data/live_deployments.json index 30a4544f3..eeb99ed77 100644 --- a/_data/live_deployments.json +++ b/_data/live_deployments.json @@ -1728,6 +1728,26 @@ "highlight": "Over 1,500 ontologies, controlled vocabularies, and resources including their preferred prefix, name, description, homepage, mappings to other registries, and more." } ] + }, + { + "name": "Metabolic Atlas", + "description": "A web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis. ", + "url": "https://metabolicatlas.org", + "nodes": ["SE"], + "profiles": [ + { + "profileName": "MolecularEntity", + "conformsTo": "0.5-RELEASE", + "exampleURL": "https://metabolicatlas.org/explore/Human-GEM/gem-browser/metabolite/MAM00217c", + "highlight": "Over 3'000 metabolites." + }, + { + "profileName": "Gene", + "conformsTo": "1.0-RELEASE", + "exampleURL": "https://metabolicatlas.org/explore/Human-GEM/gem-browser/gene/ENSG00000078237", + "highlight": "Over 15'000 genes from multiple organisms." + } + ] } ] } From fd235516c29d57553fc55ba96230819fac92a666 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:19:49 +0200 Subject: [PATCH 07/40] Add page and people for ML group --- pages/_groups/MachineLerning.md | 42 +++++++++++++++++++ pages/_people/DanSKatz | 11 +++++ pages/_people/FotisPsomopoulos.md | 11 +++++ .../{LeylaGarcia.md => LeylaJaelCastro.md} | 0 4 files changed, 64 insertions(+) create mode 100644 pages/_groups/MachineLerning.md create mode 100644 pages/_people/DanSKatz create mode 100644 pages/_people/FotisPsomopoulos.md rename pages/_people/{LeylaGarcia.md => LeylaJaelCastro.md} (100%) diff --git a/pages/_groups/MachineLerning.md b/pages/_groups/MachineLerning.md new file mode 100644 index 000000000..4cb366088 --- /dev/null +++ b/pages/_groups/MachineLerning.md @@ -0,0 +1,42 @@ +--- +layout: group-details +identifier: machinelearning +name: Machine Learning +collection: groups +active: true +type: generic +description: Specification for digital objects commonly used in machine learning solutions. +lead: +- person: LeylaGarcia +- person: FotisPsomopoulos +- person: DanKatz +email: enquiries@bioschemas.org +issues: https://github.com/Bioschemas/bioschemas/issues?q=is%3Aopen+label%3A%22type%3A%20Dataset%22,%22type%3A%20tool%22 +folder: https://drive.google.com/drive/folders/1NGiDfc6WSCJNDheGhYApfEVN3-X6Uj6z?usp=sharing + +# Page attributes +abstract: 'Machine Learning combines data, software, models and workflows. There is a need to harmonize and connect those different elements to have a full picture of a Machine Learning approach from the metadata perspective.' +objectives: + [ + 'Describe training datasets including characterization of features and attributes that can be used for training (e.g., number of data points, classes, target variable).', + 'Describe software used for training purposes including elements related to the optimization process.', + 'Describe ML models together with their evaluation.', + 'Describe links among the different elements involved in ML approaches clearly and explicitly.' + ] + +specifications: + [ + 'Dataset', 'ComputationalTool' + ] + + +members: +- AlbanGaignard + +--- + +

Further Details

+ +

Machine Learning (ML) are nowadays a common path in data-driven research due to the amount of available data and the resources needed to process it and make sense out of it. In addition to data, software also plays and important role in ML. Models produced by an ML training process also become a thing on their own, a thing that could be seen as similar to software (e.g., prediction model that can be executed with some input and produce a prediction as output) or to data (e.g., clusters emerged from a clustering approach). Furthermore, the training software has to be tuned and optimized while the model has to be evaluted, either intrinsic or extrinsic. Ideally, all of this information should be reported and represented as metadata of the ML process. However, this is not always the case. This group, a joint effort across Research Data Alliance FAIR4ML Interest Group, ELIXIR Machine Learning Focus Group and NFDI4DataScience, aims at providing a common ground for the metadata necessary to describe ML approaches.

+ +

To achieve its objectives, this group is using as a starting point Machine Learning Cards for models and datasets. Other efforst will also be taken into account, e.g., Data, Optimization, Model and Evaluation (DOME) recommendations and AIMe registry for artificial intelligence in biomedical research.

diff --git a/pages/_people/DanSKatz b/pages/_people/DanSKatz new file mode 100644 index 000000000..5f8623943 --- /dev/null +++ b/pages/_people/DanSKatz @@ -0,0 +1,11 @@ +--- +layout: person-details +id: DanSKatz +first-name: Daniel S. +last-name: Katz +collection: people +affiliation: +homepage: +github_username: +orcid: 0000-0001-5934-7525 +--- diff --git a/pages/_people/FotisPsomopoulos.md b/pages/_people/FotisPsomopoulos.md new file mode 100644 index 000000000..18818a529 --- /dev/null +++ b/pages/_people/FotisPsomopoulos.md @@ -0,0 +1,11 @@ +--- +layout: person-details +id: LeylaJaelCastro +first-name: Fotis E. +last-name: Psomopoulos +collection: people +affiliation: +homepage: +github_username: fpsom +orcid: 0000-0002-0222-4273 +--- diff --git a/pages/_people/LeylaGarcia.md b/pages/_people/LeylaJaelCastro.md similarity index 100% rename from pages/_people/LeylaGarcia.md rename to pages/_people/LeylaJaelCastro.md From 6f43d2bff10f4fa10cd8e734c841b1d82787135d Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:29:59 +0200 Subject: [PATCH 08/40] Revert change of people file name --- pages/_people/{LeylaJaelCastro.md => LeylaGarcia.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename pages/_people/{LeylaJaelCastro.md => LeylaGarcia.md} (100%) diff --git a/pages/_people/LeylaJaelCastro.md b/pages/_people/LeylaGarcia.md similarity index 100% rename from pages/_people/LeylaJaelCastro.md rename to pages/_people/LeylaGarcia.md From a1e9bb6b365b66b450101226008a6091250419b6 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:33:48 +0200 Subject: [PATCH 09/40] Update MachineLerning.md --- pages/_groups/MachineLerning.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/_groups/MachineLerning.md b/pages/_groups/MachineLerning.md index 4cb366088..c818317fd 100644 --- a/pages/_groups/MachineLerning.md +++ b/pages/_groups/MachineLerning.md @@ -11,7 +11,7 @@ lead: - person: FotisPsomopoulos - person: DanKatz email: enquiries@bioschemas.org -issues: https://github.com/Bioschemas/bioschemas/issues?q=is%3Aopen+label%3A%22type%3A%20Dataset%22,%22type%3A%20tool%22 +issues: https://github.com/BioSchemas/specifications/labels/group%3AMachineLearning folder: https://drive.google.com/drive/folders/1NGiDfc6WSCJNDheGhYApfEVN3-X6Uj6z?usp=sharing # Page attributes From 6c07c8bb871de0b54ef4b3dd865313d0841cc7d9 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:34:43 +0200 Subject: [PATCH 10/40] Update MachineLerning.md --- pages/_groups/MachineLerning.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/_groups/MachineLerning.md b/pages/_groups/MachineLerning.md index c818317fd..84e2b3b24 100644 --- a/pages/_groups/MachineLerning.md +++ b/pages/_groups/MachineLerning.md @@ -9,7 +9,7 @@ description: Specification for digital objects commonly used in machine learning lead: - person: LeylaGarcia - person: FotisPsomopoulos -- person: DanKatz +- person: DanSKatz email: enquiries@bioschemas.org issues: https://github.com/BioSchemas/specifications/labels/group%3AMachineLearning folder: https://drive.google.com/drive/folders/1NGiDfc6WSCJNDheGhYApfEVN3-X6Uj6z?usp=sharing From 47acae949e40b18f083c1464a332af85cc529fda Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:38:16 +0200 Subject: [PATCH 11/40] Add file extension to people page --- pages/_people/{DanSKatz => DanSKatz.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename pages/_people/{DanSKatz => DanSKatz.md} (100%) diff --git a/pages/_people/DanSKatz b/pages/_people/DanSKatz.md similarity index 100% rename from pages/_people/DanSKatz rename to pages/_people/DanSKatz.md From 882097e95fb3f70f594b06209ca943e43df44818 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:41:13 +0200 Subject: [PATCH 12/40] Update MachineLerning.md --- pages/_groups/MachineLerning.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pages/_groups/MachineLerning.md b/pages/_groups/MachineLerning.md index 84e2b3b24..5ad50eaa6 100644 --- a/pages/_groups/MachineLerning.md +++ b/pages/_groups/MachineLerning.md @@ -7,9 +7,9 @@ active: true type: generic description: Specification for digital objects commonly used in machine learning solutions. lead: -- person: LeylaGarcia -- person: FotisPsomopoulos -- person: DanSKatz + - LeylaGarcia + - FotisPsomopoulos + - DanSKatz email: enquiries@bioschemas.org issues: https://github.com/BioSchemas/specifications/labels/group%3AMachineLearning folder: https://drive.google.com/drive/folders/1NGiDfc6WSCJNDheGhYApfEVN3-X6Uj6z?usp=sharing From 3daf9296a7e6fc4f912b5e18d4cf478b221b7611 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:43:01 +0200 Subject: [PATCH 13/40] Update MachineLerning.md --- pages/_groups/MachineLerning.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pages/_groups/MachineLerning.md b/pages/_groups/MachineLerning.md index 5ad50eaa6..85bfb90b6 100644 --- a/pages/_groups/MachineLerning.md +++ b/pages/_groups/MachineLerning.md @@ -7,9 +7,9 @@ active: true type: generic description: Specification for digital objects commonly used in machine learning solutions. lead: - - LeylaGarcia - - FotisPsomopoulos - - DanSKatz + - person: LeylaGarcia + - person: FotisPsomopoulos + - person: DanSKatz email: enquiries@bioschemas.org issues: https://github.com/BioSchemas/specifications/labels/group%3AMachineLearning folder: https://drive.google.com/drive/folders/1NGiDfc6WSCJNDheGhYApfEVN3-X6Uj6z?usp=sharing From c2d4c22105ca128ba65e2267880ce62eb165bcc0 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:45:37 +0200 Subject: [PATCH 14/40] Testing --- _layouts/person-details.html | 3 +++ 1 file changed, 3 insertions(+) diff --git a/_layouts/person-details.html b/_layouts/person-details.html index 06617c168..50f78a1b5 100644 --- a/_layouts/person-details.html +++ b/_layouts/person-details.html @@ -24,6 +24,9 @@

Groups

    {% for group in site.groups %} + {% for person in group.lead %} + person + {% endfor %} {% if group.lead contains person-id %}
  • {{group.name}}

    From 213e1f862abd681804d77bfa97c2c7da941976f5 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:47:04 +0200 Subject: [PATCH 15/40] Testing --- _layouts/person-details.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_layouts/person-details.html b/_layouts/person-details.html index 50f78a1b5..cb3e95c14 100644 --- a/_layouts/person-details.html +++ b/_layouts/person-details.html @@ -25,7 +25,7 @@

    Groups

      {% for group in site.groups %} {% for person in group.lead %} - person + {{person}} {% endfor %} {% if group.lead contains person-id %}
    • From 8bdb2b712f76b315810c9017b7e54f1ec7c2c208 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:52:28 +0200 Subject: [PATCH 16/40] Testing --- _layouts/person-details.html | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/_layouts/person-details.html b/_layouts/person-details.html index cb3e95c14..8f5c39932 100644 --- a/_layouts/person-details.html +++ b/_layouts/person-details.html @@ -25,13 +25,13 @@

      Groups

        {% for group in site.groups %} {% for person in group.lead %} - {{person}} + {{ person.person }} + {% if person contains person-id %} +
      • + {{group.name}}

        +
        • + {% endif %} {% endfor %} - {% if group.lead contains person-id %} -
      • - {{group.name}}

        -
        • - {% endif %} {% if group.members contains person-id %}
      • {{group.name}}

        From d33a5ef29fab2322d153a56363136fbcb8342822 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 12:57:40 +0200 Subject: [PATCH 17/40] Testing --- _layouts/person-details.html | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/_layouts/person-details.html b/_layouts/person-details.html index 8f5c39932..7b0be389b 100644 --- a/_layouts/person-details.html +++ b/_layouts/person-details.html @@ -24,20 +24,19 @@

        Groups

         From 714d05a8bddffcaaa710418349d97def6df5ce25 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 14:07:37 +0200 Subject: [PATCH 18/40] Add SMP case and related people --- pages/_groups/Tools.md | 16 ++++++++++++++-- pages/_people/AllegraVia.md | 9 +++++++++ pages/_people/DimitriosBampalikis.md | 9 +++++++++ pages/_people/EvaMartin.md | 9 +++++++++ 4 files changed, 41 insertions(+), 2 deletions(-) create mode 100644 pages/_people/AllegraVia.md create mode 100644 pages/_people/DimitriosBampalikis.md create mode 100644 pages/_people/EvaMartin.md diff --git a/pages/_groups/Tools.md b/pages/_groups/Tools.md index 85bb8f715..5fd729070 100755 --- a/pages/_groups/Tools.md +++ b/pages/_groups/Tools.md @@ -5,8 +5,10 @@ name: Tools collection: groups active: true type: generic -description: Specification for tools +description: Specification for computational tools, e.g., software applications, software releases and software source code lead: +- person: FotisPsomopoulos +- person: EvaMartin - person: RicardoArcila - person: JustinClark-Casey - person: LeylaGarcia @@ -18,7 +20,8 @@ folder: https://drive.google.com/open?id=0BzDhyOWTnRNTYkdQNHppUjZ3U2M abstract: 'The Tools Group develops and maintains a community specification for describing life science tools.' objectives: [ - 'This group investigates the required extensions to schema.org to support such use case.' + 'This group investigates the required extensions to schema.org to support the description of software tools, applications, releaseas and source code.', + 'A specific use case is supporting machine-actionable Software Management Plans' ] specifications: @@ -28,6 +31,9 @@ specifications: members: + - JoseMFernandez + - AllegraVia + - DimitriosBampakalis - GiuseppeProfiti - NiallBeard - PhilippeRocca-Serra @@ -55,3 +61,9 @@ members: - StianSoiland-Reyes - SaharFrikha --- + +

        Further Details

        + +

        Research software is a fundamental element in research. Research software recognition and citation, together with software management plans will improve reproducibility in science.

        + +

        For the specific use case around machine-actionable software management plans, this group has taken as a starting point the metadata schemas produced as part of the maSMPs project lead by the Semantic Technologies group at ZB MED and funded by RDA/EOSC-Future horizon 2020 Framework Programme no. 101017536. Such metadata schemas were created taking as basis the ELIXIR SMPs created by the ELIXIR Software Best Practices group, and later aligned to other related efforts (e.g., SMPs in RDMO, SMPs by eScience Center Netherlands). The maSMPs also take into account the maDMPs produced by the RDA-DMP-Common-Standard.

        diff --git a/pages/_people/AllegraVia.md b/pages/_people/AllegraVia.md new file mode 100644 index 000000000..8a85a3d91 --- /dev/null +++ b/pages/_people/AllegraVia.md @@ -0,0 +1,9 @@ +--- +layout: person-details +id: AllegraVia +first-name: Allegra +last-name: Via +collection: people +affiliation: +orcid: 0000-0002-3398-5462 +--- diff --git a/pages/_people/DimitriosBampalikis.md b/pages/_people/DimitriosBampalikis.md new file mode 100644 index 000000000..1be9871f9 --- /dev/null +++ b/pages/_people/DimitriosBampalikis.md @@ -0,0 +1,9 @@ +--- +layout: person-details +id: DimitriosBampalikis +first-name: Dimitrios +last-name: Bampalikis +collection: people +affiliation: +orcid: +--- diff --git a/pages/_people/EvaMartin.md b/pages/_people/EvaMartin.md new file mode 100644 index 000000000..332840767 --- /dev/null +++ b/pages/_people/EvaMartin.md @@ -0,0 +1,9 @@ +--- +layout: person-details +id: EvaMartin +first-name: Eva +last-name: Martin del Pico +collection: people +affiliation: +orcid: 0000-0001-8324-2897 +--- From 9081d94f4fb9bbd0c9812adf0cb5a896fc2d117e Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 14:08:27 +0200 Subject: [PATCH 19/40] fix typo --- pages/_groups/{MachineLerning.md => MachineLearning.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename pages/_groups/{MachineLerning.md => MachineLearning.md} (100%) diff --git a/pages/_groups/MachineLerning.md b/pages/_groups/MachineLearning.md similarity index 100% rename from pages/_groups/MachineLerning.md rename to pages/_groups/MachineLearning.md From e8b8135aa3f147947fea533b5948ed9272f797ae Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 14:09:31 +0200 Subject: [PATCH 20/40] Fix typo --- pages/_groups/{MachineLerning.md => MachineLearning.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename pages/_groups/{MachineLerning.md => MachineLearning.md} (100%) diff --git a/pages/_groups/MachineLerning.md b/pages/_groups/MachineLearning.md similarity index 100% rename from pages/_groups/MachineLerning.md rename to pages/_groups/MachineLearning.md From 041fc03d3ed7044354c2837948d5386cff3e8a95 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 14:12:35 +0200 Subject: [PATCH 21/40] Update Tools.md --- pages/_groups/Tools.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pages/_groups/Tools.md b/pages/_groups/Tools.md index 5fd729070..944791f41 100755 --- a/pages/_groups/Tools.md +++ b/pages/_groups/Tools.md @@ -34,6 +34,8 @@ members: - JoseMFernandez - AllegraVia - DimitriosBampakalis + - OlgaXimenaGiraldo + - DietrichRebholzSchuhmann - GiuseppeProfiti - NiallBeard - PhilippeRocca-Serra From 6a941a54e58b965705ff1df6d9b0ea9bf649f23b Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 14:17:47 +0200 Subject: [PATCH 22/40] Update MachineLearning.md --- pages/_groups/MachineLearning.md | 1 + 1 file changed, 1 insertion(+) diff --git a/pages/_groups/MachineLearning.md b/pages/_groups/MachineLearning.md index 85bfb90b6..f69c37802 100644 --- a/pages/_groups/MachineLearning.md +++ b/pages/_groups/MachineLearning.md @@ -32,6 +32,7 @@ specifications: members: - AlbanGaignard +- DietrichRebholzSchuhmann --- From 9ae5492c395e3d274316ff5548d2b3e1d6ff19ad Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Sun, 25 Jun 2023 14:19:04 +0200 Subject: [PATCH 23/40] Update MachineLearning.md --- pages/_groups/MachineLearning.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/_groups/MachineLearning.md b/pages/_groups/MachineLearning.md index 85bfb90b6..af5837608 100644 --- a/pages/_groups/MachineLearning.md +++ b/pages/_groups/MachineLearning.md @@ -32,7 +32,7 @@ specifications: members: - AlbanGaignard - +- DietrichRebholzSchuhmann ---

        Further Details

        From 7d2e5a345650e1b7af145099a7b40ce62463c2f3 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Mon, 26 Jun 2023 14:23:45 +0200 Subject: [PATCH 24/40] Add new member --- pages/_groups/MachineLearning.md | 1 + 1 file changed, 1 insertion(+) diff --git a/pages/_groups/MachineLearning.md b/pages/_groups/MachineLearning.md index f69c37802..6459a9161 100644 --- a/pages/_groups/MachineLearning.md +++ b/pages/_groups/MachineLearning.md @@ -33,6 +33,7 @@ specifications: members: - AlbanGaignard - DietrichRebholzSchuhmann +- IvanMicetic --- From 5212706a677c73360bbc55e4398ad313f1d510af Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Mon, 26 Jun 2023 19:51:06 +0200 Subject: [PATCH 25/40] Add links and fix copy/paste error --- pages/_groups/MachineLearning.md | 2 +- pages/_people/FotisPsomopoulos.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/_groups/MachineLearning.md b/pages/_groups/MachineLearning.md index 6459a9161..fa0c2296a 100644 --- a/pages/_groups/MachineLearning.md +++ b/pages/_groups/MachineLearning.md @@ -41,4 +41,4 @@ members:

        Machine Learning (ML) are nowadays a common path in data-driven research due to the amount of available data and the resources needed to process it and make sense out of it. In addition to data, software also plays and important role in ML. Models produced by an ML training process also become a thing on their own, a thing that could be seen as similar to software (e.g., prediction model that can be executed with some input and produce a prediction as output) or to data (e.g., clusters emerged from a clustering approach). Furthermore, the training software has to be tuned and optimized while the model has to be evaluted, either intrinsic or extrinsic. Ideally, all of this information should be reported and represented as metadata of the ML process. However, this is not always the case. This group, a joint effort across Research Data Alliance FAIR4ML Interest Group, ELIXIR Machine Learning Focus Group and NFDI4DataScience, aims at providing a common ground for the metadata necessary to describe ML approaches.

        -

        To achieve its objectives, this group is using as a starting point Machine Learning Cards for models and datasets. Other efforst will also be taken into account, e.g., Data, Optimization, Model and Evaluation (DOME) recommendations and AIMe registry for artificial intelligence in biomedical research.

        +

        To achieve its objectives, this group is using as a starting point Machine Learning Cards for models and datasets. Other efforst will also be taken into account, e.g., Data, Optimization, Model and Evaluation (DOME) recommendations, AIMe registry for artificial intelligence in biomedical research and HuggingFace.

        diff --git a/pages/_people/FotisPsomopoulos.md b/pages/_people/FotisPsomopoulos.md index 18818a529..9954ed145 100644 --- a/pages/_people/FotisPsomopoulos.md +++ b/pages/_people/FotisPsomopoulos.md @@ -1,6 +1,6 @@ --- layout: person-details -id: LeylaJaelCastro +id: FotisPsomopoulos first-name: Fotis E. last-name: Psomopoulos collection: people From 2b57f9559933822a4cb9bffab9786c4cf714bfa5 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Mon, 26 Jun 2023 19:52:05 +0200 Subject: [PATCH 26/40] Fix copy/paste error --- pages/_people/FotisPsomopoulos.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/_people/FotisPsomopoulos.md b/pages/_people/FotisPsomopoulos.md index 18818a529..9954ed145 100644 --- a/pages/_people/FotisPsomopoulos.md +++ b/pages/_people/FotisPsomopoulos.md @@ -1,6 +1,6 @@ --- layout: person-details -id: LeylaJaelCastro +id: FotisPsomopoulos first-name: Fotis E. last-name: Psomopoulos collection: people From 058adf19b6d80803f36f6a0bbbab491edd477877 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Mon, 26 Jun 2023 19:56:21 +0200 Subject: [PATCH 27/40] Add suggestions by Alves --- pages/_groups/MachineLearning.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/_groups/MachineLearning.md b/pages/_groups/MachineLearning.md index fa0c2296a..bca448116 100644 --- a/pages/_groups/MachineLearning.md +++ b/pages/_groups/MachineLearning.md @@ -39,6 +39,6 @@ members:

        Further Details

        -

        Machine Learning (ML) are nowadays a common path in data-driven research due to the amount of available data and the resources needed to process it and make sense out of it. In addition to data, software also plays and important role in ML. Models produced by an ML training process also become a thing on their own, a thing that could be seen as similar to software (e.g., prediction model that can be executed with some input and produce a prediction as output) or to data (e.g., clusters emerged from a clustering approach). Furthermore, the training software has to be tuned and optimized while the model has to be evaluted, either intrinsic or extrinsic. Ideally, all of this information should be reported and represented as metadata of the ML process. However, this is not always the case. This group, a joint effort across Research Data Alliance FAIR4ML Interest Group, ELIXIR Machine Learning Focus Group and NFDI4DataScience, aims at providing a common ground for the metadata necessary to describe ML approaches.

        +

        Machine Learning (ML) is nowadays a common path in data-driven research due to the amount of available data and the resources needed to process it and make sense out of it. In addition to data, software also plays and important role in ML. Models produced by an ML training process also become a thing on their own, a thing that could be seen as similar to software (e.g., prediction model that can be executed with some input and produce a prediction as output) or to data (e.g., clusters emerged from a clustering approach). Furthermore, the training software has to be tuned and optimized while the model has to be evaluted, either intrinsic or extrinsically. Ideally, all of this information should be reported and represented as metadata of the ML process. However, this is not always the case. This group, a joint effort across Research Data Alliance FAIR4ML Interest Group, ELIXIR Machine Learning Focus Group and NFDI4DataScience, aims at providing a common ground for the metadata necessary to describe ML approaches.

        To achieve its objectives, this group is using as a starting point Machine Learning Cards for models and datasets. Other efforst will also be taken into account, e.g., Data, Optimization, Model and Evaluation (DOME) recommendations, AIMe registry for artificial intelligence in biomedical research and HuggingFace.

        From fab3bd0434ccb3486a73c31866fd5006f0bdc1bd Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Tue, 27 Jun 2023 16:03:24 +0200 Subject: [PATCH 28/40] Update pages/_groups/Tools.md Co-authored-by: Renato Alves --- pages/_groups/Tools.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/_groups/Tools.md b/pages/_groups/Tools.md index 944791f41..d9af4c2ac 100755 --- a/pages/_groups/Tools.md +++ b/pages/_groups/Tools.md @@ -20,7 +20,7 @@ folder: https://drive.google.com/open?id=0BzDhyOWTnRNTYkdQNHppUjZ3U2M abstract: 'The Tools Group develops and maintains a community specification for describing life science tools.' objectives: [ - 'This group investigates the required extensions to schema.org to support the description of software tools, applications, releaseas and source code.', + 'This group investigates the required extensions to schema.org to support the description of software tools, applications, releases and source code.', 'A specific use case is supporting machine-actionable Software Management Plans' ] From a88199aa810561b5ef3684762e7e506e5c38ac12 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Wed, 28 Jun 2023 10:38:51 +0200 Subject: [PATCH 29/40] Update Tools.md --- pages/_groups/Tools.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/_groups/Tools.md b/pages/_groups/Tools.md index d9af4c2ac..198852995 100755 --- a/pages/_groups/Tools.md +++ b/pages/_groups/Tools.md @@ -21,7 +21,7 @@ abstract: 'The Tools Group develops and maintains a community specification for objectives: [ 'This group investigates the required extensions to schema.org to support the description of software tools, applications, releases and source code.', - 'A specific use case is supporting machine-actionable Software Management Plans' + 'A specific use case is supporting machine-actionable Software Management Plans (maSMPS)' ] specifications: @@ -68,4 +68,4 @@ members:

        Research software is a fundamental element in research. Research software recognition and citation, together with software management plans will improve reproducibility in science.

        -

        For the specific use case around machine-actionable software management plans, this group has taken as a starting point the metadata schemas produced as part of the maSMPs project lead by the Semantic Technologies group at ZB MED and funded by RDA/EOSC-Future horizon 2020 Framework Programme no. 101017536. Such metadata schemas were created taking as basis the ELIXIR SMPs created by the ELIXIR Software Best Practices group, and later aligned to other related efforts (e.g., SMPs in RDMO, SMPs by eScience Center Netherlands). The maSMPs also take into account the maDMPs produced by the RDA-DMP-Common-Standard.

        +

        For the specific use case around machine-actionable software management plans, this group has taken as a starting point the metadata schemas produced as part of the maSMPs project lead by the Semantic Technologies group at ZB MED, with funding from RDA/EOSC-Future horizon 2020 Framework Programme (no. 101017536) and Deutsche Forschungsgemeinschaft DFG (project no. 460234259 corresponding to the NFDI4DataScience consortium). Such metadata schemas were created taking as basis the ELIXIR SMPs created by the ELIXIR Software Best Practices group, and later aligned to other related efforts (e.g., SMPs in RDMO, SMPs by eScience Center Netherlands). The maSMPs also take into account the maDMPs produced by the RDA-DMP-Common-Standard.

        From 8c9096e0711726aa2b086eb961fb78299848adf0 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Wed, 28 Jun 2023 10:41:42 +0200 Subject: [PATCH 30/40] Update Tools.md --- pages/_groups/Tools.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/_groups/Tools.md b/pages/_groups/Tools.md index 198852995..3b53374e5 100755 --- a/pages/_groups/Tools.md +++ b/pages/_groups/Tools.md @@ -68,4 +68,4 @@ members:

        Research software is a fundamental element in research. Research software recognition and citation, together with software management plans will improve reproducibility in science.

        -

        For the specific use case around machine-actionable software management plans, this group has taken as a starting point the metadata schemas produced as part of the maSMPs project lead by the Semantic Technologies group at ZB MED, with funding from RDA/EOSC-Future horizon 2020 Framework Programme (no. 101017536) and Deutsche Forschungsgemeinschaft DFG (project no. 460234259 corresponding to the NFDI4DataScience consortium). Such metadata schemas were created taking as basis the ELIXIR SMPs created by the ELIXIR Software Best Practices group, and later aligned to other related efforts (e.g., SMPs in RDMO, SMPs by eScience Center Netherlands). The maSMPs also take into account the maDMPs produced by the RDA-DMP-Common-Standard.

        +

        For the specific use case around machine-actionable software management plans, this group has taken as a starting point the metadata schemas produced as part of the maSMPs project lead by the Semantic Technologies group at ZB MED, with funding from RDA/EOSC-Future horizon 2020 Framework Programme (no. 101017536) and Deutsche Forschungsgemeinschaft DFG (project no. 460234259 corresponding to the NFDI4DataScience consortium). Such metadata schemas were created taking as basis the ELIXIR SMPs created by the ELIXIR Software Best Practices group, and later aligned to other related efforts (e.g., SMPs in RDMO, SMPs by eScience Center Netherlands). The maSMPs also take into account the maDMPs produced by the RDA-DMP-Common-Standard.

        From 9b20ecfc4b783af45601fc54af3e413a787b0d2c Mon Sep 17 00:00:00 2001 From: gtsueng Date: Wed, 12 Jul 2023 08:11:20 -0700 Subject: [PATCH 31/40] Update 1.1-DRAFT.html Fix sameAs description --- pages/_profiles/TrainingMaterial/1.1-DRAFT.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/_profiles/TrainingMaterial/1.1-DRAFT.html b/pages/_profiles/TrainingMaterial/1.1-DRAFT.html index a51089d74..453d38334 100644 --- a/pages/_profiles/TrainingMaterial/1.1-DRAFT.html +++ b/pages/_profiles/TrainingMaterial/1.1-DRAFT.html @@ -253,7 +253,7 @@ - bsc_description: '' cardinality: MANY controlled_vocab: '' - description: URL of additional sources for the dataset + description: URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website. example: '' expected_types: - URL @@ -452,4 +452,4 @@ spec_type: Profile status: revision use_cases_url: /useCases/TrainingMaterial ---- \ No newline at end of file +--- From 73afd393736eb26ca9555cb8272ac028f0ae6f61 Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Thu, 13 Jul 2023 16:28:56 +0200 Subject: [PATCH 32/40] No twitter --- index.html | 4 ---- 1 file changed, 4 deletions(-) diff --git a/index.html b/index.html index 9998bae53..5b496c529 100644 --- a/index.html +++ b/index.html @@ -132,10 +132,6 @@

        Latest Presentation

        See more presentations and publications.
        -
        - - -
        From 9b717998c76278453bb8bcd0f5fb4a62a7fd639d Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Thu, 13 Jul 2023 16:31:03 +0200 Subject: [PATCH 33/40] Update index.html --- index.html | 1 - 1 file changed, 1 deletion(-) diff --git a/index.html b/index.html index 5b496c529..45d4c76b6 100644 --- a/index.html +++ b/index.html @@ -131,7 +131,6 @@

        Latest Presentation

        See more presentations and publications. -
        From 6973785cb4f35db9ead43248b66d57f0abe461c9 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Tue, 18 Jul 2023 18:39:32 +0200 Subject: [PATCH 34/40] Update index.html --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index 9998bae53..ae3ab40c6 100644 --- a/index.html +++ b/index.html @@ -8,7 +8,7 @@ title: Bioschemas # Community Call details call-minutes: https://docs.google.com/document/d/1kd5F97ogdiPNhLTnkei-RVR8TC8Ohpc5QSPX3KsfDrk -call-date: 2023-06-26T15:00UTC +call-date: 2023-07-24T15:00UTC ---
        From 9183a4128af52d283bd9973e021dcd611537e1bc Mon Sep 17 00:00:00 2001 From: M-casado Date: Fri, 28 Jul 2023 11:14:51 +0100 Subject: [PATCH 35/40] Amend missing insulin image --- pages/_tutorials/what_why_bioschemas.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/_tutorials/what_why_bioschemas.md b/pages/_tutorials/what_why_bioschemas.md index a0c02c470..2332b1cce 100644 --- a/pages/_tutorials/what_why_bioschemas.md +++ b/pages/_tutorials/what_why_bioschemas.md @@ -49,7 +49,7 @@ Using schema.org markup on web pages enables the generation of 'info box' summar Imagine an insulin summary appearing within search results, but rather than pointing to Wikipedia, that summary would direct one to specialized resources such as Orphanet or CATH as seen in Figure 1. In this way you would get a quick overview while also being provided links to relevant resources, all in one search. -{% include image.html file="/tutorials/images/ilustration_life_sciences_event.png" caption="Figure 1. Insulin summary on a search engine" alt="Insulin summary on a search engine" %} +{% include image.html file="/tutorials/images/insulin.png" caption="Figure 1. Insulin summary on a search engine" alt="Insulin summary on a search engine" %} ## 2. What are the benefits of Bioschemas? From e313061b5f891b34c2e4b9cdb940e88b9054a810 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Wed, 16 Aug 2023 16:01:06 +0200 Subject: [PATCH 36/40] no BMUSE --- _includes/live-deploy-site-info.html | 5 ----- pages/_developer/liveDeploys.html | 11 +---------- 2 files changed, 1 insertion(+), 15 deletions(-) diff --git a/_includes/live-deploy-site-info.html b/_includes/live-deploy-site-info.html index ccfb72a35..3c49f8b17 100644 --- a/_includes/live-deploy-site-info.html +++ b/_includes/live-deploy-site-info.html @@ -67,11 +67,6 @@

        Implemented Profiles

        SMV
        {%- endif %} - {%- if profile.exampleURL != nil %} -
        - BMUSE -
        - {%- endif %} {%- endfor %} diff --git a/pages/_developer/liveDeploys.html b/pages/_developer/liveDeploys.html index 0f96549dd..1c2d69fd3 100644 --- a/pages/_developer/liveDeploys.html +++ b/pages/_developer/liveDeploys.html @@ -6,12 +6,11 @@ - "/liveDeploys" exampleHoverText: "View example page" schemaHoverText: "Visualise on the Schema.org Markup Validation Tool (SMV)" -bmuseHoverText: "Retrieve using Bioschemas Scraping service" --- {%- assign count = 0 %}

        {{ page.title }}

        -

        Below we list the sites that use Bioschemas markup to describe what they are offering. We provide a direct link to the site, an example deployment page, a link to test the markup syntax using the Schema.org Markup Validation tool (SMV), and also a link to the results of using the Bioschemas Markup Scraper and Extractor tool (BMUSE). The links to the Schema.org Markup Validation tool and BMUSE show one example page from the site; however, many more may exist.

        +

        Below we list the sites that use Bioschemas markup to describe what they are offering. We provide a direct link to the site, an example deployment page and a link to test the markup syntax using the Schema.org Markup Validation tool (SMV).

        Note that when using the Schema.org Markup Validator, you may encounter some error warnings for types and properties. These should correspond to the types and properties that are being proposed by Bioschemas as extensions to the Schema.org vocabulary.

        @@ -104,9 +103,6 @@

        SMV
        -
        - BMUSE -
        {%- endif %} {%- break %} {%- endif %} @@ -248,11 +244,6 @@

        Implemented Profiles

        SMV {%- endif %} - {%- if profile.exampleURL != nil %} -
        - BMUSE -
        - {%- endif %} {%- endfor %} From c42b1f9d41717813142b9556759fad7c7877bbb2 Mon Sep 17 00:00:00 2001 From: Steffen Neumann Date: Sun, 3 Sep 2023 11:39:47 +0200 Subject: [PATCH 37/40] Update live_deployment for MassBank Follow change from MolecularEntity to ChemicalSubstance Update datadump URL to latest artifact from CI Update example links to the records with accession schema --- _data/live_deployments.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/_data/live_deployments.json b/_data/live_deployments.json index eeb99ed77..5f3eee9f7 100644 --- a/_data/live_deployments.json +++ b/_data/live_deployments.json @@ -1175,17 +1175,17 @@ "url": "https://massbank.eu/MassBank/", "nodes": "DE", "sitemap": "https://massbank.eu/MassBank/sitemapindex.xml", - "datadump": "https://msbi.ipb-halle.de/~sneumann/MassBank-2006.06.jsonld", + "datadump": "https://github.com/MassBank/MassBank-data/releases/latest/download/MassBank.json", "profiles": [ { - "profileName": "MolecularEntity", - "conformsTo": "0.5", - "exampleURL": "https://massbank.eu/MassBank/RecordDisplay?id=LQB00001&dsn=RIKEN_IMS" + "profileName": "ChemicalSubstance", + "conformsTo": "0.4-RELEASE", + "exampleURL": "https://massbank.eu/MassBank/RecordDisplay?id=MSBNK-RIKEN_IMS-LQB00001" }, { "profileName": "Dataset", - "conformsTo": "0.3", - "exampleURL": "https://massbank.eu/MassBank/RecordDisplay?id=LQB00001&dsn=RIKEN_IMS" + "conformsTo": "1.0-RELEASE", + "exampleURL": "https://massbank.eu/MassBank/RecordDisplay?id=MSBNK-RIKEN_IMS-LQB00001" } ] }, From d9fb2eb9ec498aacbdf161bef45bbaeba657ead0 Mon Sep 17 00:00:00 2001 From: ljgarcia Date: Wed, 6 Sep 2023 13:18:35 +0200 Subject: [PATCH 38/40] Update ChrisChild.md Removes GitHub user and webpage as both were giving errors --- pages/_people/ChrisChild.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/pages/_people/ChrisChild.md b/pages/_people/ChrisChild.md index 7f32bd9f0..8a3e55c5d 100644 --- a/pages/_people/ChrisChild.md +++ b/pages/_people/ChrisChild.md @@ -5,7 +5,5 @@ first-name: Chris last-name: Child collection: people affiliation: The University of Manchester -homepage: https://hardcopy.dev/ -github_username: christopherchild orcid: 0000-0003-0758-6908 --- From 4623ed17bba9cc829b108f8efec0edd58622829f Mon Sep 17 00:00:00 2001 From: Alban Gaignard Date: Fri, 15 Sep 2023 11:19:10 +0200 Subject: [PATCH 39/40] next community call --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index 4dd2e705f..b3ed85101 100644 --- a/index.html +++ b/index.html @@ -8,7 +8,7 @@ title: Bioschemas # Community Call details call-minutes: https://docs.google.com/document/d/1kd5F97ogdiPNhLTnkei-RVR8TC8Ohpc5QSPX3KsfDrk -call-date: 2023-07-24T15:00UTC +call-date: 2023-09-25T15:00UTC ---
        From 9ae16755e6b0b705f62a5e30d85edd98965a606f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 25 Sep 2023 17:27:50 +0200 Subject: [PATCH 40/40] Added a recent presentation --- _data/presentations.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/_data/presentations.csv b/_data/presentations.csv index 23df181e5..254d72cf9 100644 --- a/_data/presentations.csv +++ b/_data/presentations.csv @@ -5,4 +5,5 @@ Bioschemas for the IDP Community,AlasdairGray,https://docs.google.com/presentati (Bio)schemas – Making (not only life science) data resources more interoperable and discoverable on the Web,AlasdairGray,https://docs.google.com/presentation/d/1TqvYpZVBvq_nhUkfzrzar6n87lDkryS-KYBf5bBH7bI/edit#slide=id.p1,2022-04_NFDI-InfraTalk,,, Contributing to EOSC Research Graphs: the role of FAIRsharing and Bioschemas,SusannaSansone,https://docs.google.com/presentation/d/1lwm-452v-pyfd7egfmh4APbX3CHXe9xu/edit#slide=id.g12f39d505fa_0_535,2022-06_ELIXIRAllHands2022,,, (Bio)schemas: Making data resources more Interoperable and Discoverable on the Web,AlasdairGray,https://docs.google.com/presentation/d/1MDWzlx4Mm1dpHOVnRlZcQqAIQuaOrvOfRVSLvArQBug/edit#slide=id.p1,2022-09_Ont4Chem,,, -Bioschemas: Marking up biodiversity websites to improve data discovery and web-scale integration,FranckMichel,https://docs.google.com/presentation/d/15HB6ldOSN5C_H10w9chwWyPt_CNh8AlM/edit#slide=id.p1,,,"NFDI4Biodiversity All Hands Conference, Workshop on Data Standards & Common Language",12-14 October 2022 \ No newline at end of file +Bioschemas: Marking up biodiversity websites to improve data discovery and web-scale integration,FranckMichel,https://docs.google.com/presentation/d/15HB6ldOSN5C_H10w9chwWyPt_CNh8AlM/edit#slide=id.p1,,,"NFDI4Biodiversity All Hands Conference, Workshop on Data Standards & Common Language",12-14 October 2022 +Improving findability on chemical resources with Bioschemas,EgonWillighagen,https://doi.org/10.5281/zenodo.8369861,,https://www.acs.org/meetings/acs-meetings/fall-2023.html,"ACS Fall 2023",13-17 August 2023