Bioschemas mapping for Lab Protocol
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Lab protocols<USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME>
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<USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL>
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Olga Giraldo<CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...>
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schema.orgbioschemas
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PropertyExpected TypeDescriptionSubPropertiesMarginalityCardinalitySuggested Controlled VocabulariesNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCase
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New properties for LabProtocol
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advantageTextIt should be made clear in which situations the Protocol has been successfully employed.RecommendedMANYadvantage"We describe a fast, efficient and economic in-house protocol for plasmid preparation using glass syringe filters. Plasmid yield and quality as determined by enzyme digestion and transfection efficiency were equivalent to the expensive commercial kits. Importantly, the time required for purification was much less than that required using a commercial kit." EXAMPLE SOURCE: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007750Match
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limitationTextIt should be made clear in which situations the Protocol would be unreliable or otherwise unsuccessful.RecommendedMANYlimitation"A major problem faced both in this and other safflower transformation studies is the hyperhydration of transgenic shoots which result in the loss of a large proportion of transgenic shoots." EXAMPE SOURCE: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115923/Match
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applicabilityTextApplications of the protocol list the full diversity of the applications of the method and support if is possible to extend the range of applications of the protocol. e.g. northern blot assays, sequencing, etc.RecommendedMANYapplicationDNA from this experiment can be used for all kinds of genetics studies, including genotyping and mapping.Match
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reagentBiologicalEntity (chemicals) or URLReagents participating in the list. ChEBI and PubChem entities can be used whenever available. Commercial names are also acceptable (URL if possible)MinimumMANYreagentReagents that are purchased ready-to-use, solutions (or mixtures) prepared in the lab, media, buffer, kits.Match
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Reused properties from MedicalDevice
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purposeTextA goal towards an action is taken. Can be concrete or abstract.MinimumMANYpurpose"Development of a method to isolate small RNAs from different plant species (…) that no need of first total RNA extraction and is not based on the commercially available TRIzol" EXAMPLE SOURCE: https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-7-4Match
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Reused properties from MedicalStudy
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outcomeTextoutcome or expected result by a protocol execution.RecommendedMANYoutcomelikely yield of protein, typical microscopy images, the expected size of an amplified product, chemical compounds synthesized as part of a procedure, etc.Match
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Reused properties from CreativeWork
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identifierPropertyValue, Text, URLThe 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.MinimumONEidentifierDOI: https://doi.org/10.21769/BioProtoc.2159; doi: 10.3791/55164; doi:10.1101/pdb.prot4765Match
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citationCreativeWork or URLA citation or reference to a creative work, such as a publication, web page, scholarly article, etc.RecommendedMANYpublication, citation, reference"This protocol is related to the following articles:
Effective detection of variation in single-cell transcriptomes using MATQ-seq
Kuanwei Sheng, Wenjian Cao, Yichi Niu, Qing Deng, and Chenghang Zong
Nature Methods doi:10.1038/nmeth.4145
". EXAMPLE SOURCE: http://cshprotocols.cshlp.org/cgi/collection/dna_isolation_in_plants
Match
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licenseCreativeWork or URLA license document that applies to this content, typically indicated by URL.MinimumONElicenseCreative Commons Attribution licence (https://creativecommons.org/licenses/by/4.0/)Match
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isBasedOnCreativeWork or
URL
A resource that was used in the creation of this resource. This term can be repeated for multiple sources. For example, http://example.com/great-multiplication-intro.html. Supersedes isBasedOnUrl.RecommendedMANYprovenance"This protocol was adapted from “How to Study Gene Expression,” Chapter 7, in Arabidopsis:A Laboratory Manual (eds. Weigel and Glazebrook). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2002." EXAMPLE SOURCE: http://cshprotocols.cshlp.org/content/2007/2/pdb.prot4690.abstractMatch
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Reused properties from Product/Service
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categoryTextA category for the item. Greater signs or slashes can be used to informally indicate a category hierarchy.RecommendedMANYcategoryBiotechnology; cancer; cell biology; computational biologyMatch
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New Properties from Thing
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isMentionedInThingCretiveWork, Dataset, collection mentioning this entity

Inverse of:mentions
RecommendedMANYsource (repository, journal, others)Bio-protocol (http://www.bio-protocol.org/e2159); JOVE (https://www.jove.com/video/55164/characterization-calcification-events-using-live-optical-electron)Match
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Reused properties from SoftwareApplication
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deviceText or URLDevice required to run the application. Used in cases where a specific make/model is required to run the application.

For LabProtocols it would be a laboratory equipment.
MinimumMANYdevice1) An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. 2) A voltmeter is a measurement device which is intended to perform some measure function. 3) next-generation sequencer is a device used to detect variants by targeted gene sequencing in, for example, cancer and genetic disorders; type a bacteria or virus; or characterize novel microbes.Match
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Reused properties from BiologicalEntity
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sampleBiologicalEntity or URLSamples used in the protocolMinimumMANYsample
The sample tested in a protocol may be an organism or a part of it. Some examples include: whole organisms such as Oriza sativa (rice), mangifera indica (mango), Mus musculus (mouse); anatomical parts like leaf, cells, tissues, membranes, organs, skeletal system, muscular system, nervous system, reproductive system, cardiovascular system; biomolecules like nucleic acids and proteins; body fluids (Blood serum, saliva, semen, amniotic fluid, cerebrospinal fluid, gastric acid, etc)
Match
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Reused properties from EntryPoint
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actionApplicationSoftwareApplicationAn application that can complete the request.RecommendedMANYsoftwareMaxQuant quantitative proteomics software (http://www.biochem.mpg.de/5111795/maxquant); ImageJ (https://imagej.nih.gov/ij/); Mapdisto (http://mapdisto.free.fr/)Match
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Reused properties from Event
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durationDurationThe time it takes to actually carry on the protocol, in ISO 8601 duration format.RecommendedONEexecution time45 min; 3 hours; 5 daysMatch
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Schema.org mapping
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