- From: Justin Clark-Casey <jc955@cam.ac.uk>
- Date: Wed, 26 Sep 2018 09:56:55 +0100
- To: Jerven.Bolleman@sib.swiss, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
- Cc: "Shimoyama, Mary" <shimoyama@mcw.edu>, "Clark, Timothy W." <TWCLARK@mgh.harvard.edu>, Rafael Jimenez <rafael.jimenez@elixir-europe.org>, Leyla Garcia <ljgarcia@ebi.ac.uk>, Dan Brickley <danbri@google.com>, public-bioschemas@w3.org, Natasha Noy <noy@google.com>, Vicki Tardif Holland <vtardif@google.com>
True. One could perhaps use CreativeWork.isPartOf or even make the parent dataset also a DataCatalog and use Dataset.includedInDataCatalog. -- Justin On 25/09/18 21:14, Jerven Tjalling Bolleman wrote: > Hi All, > > I just wanted to note that > > <script type="application/ld+json"> > { "@context" : "http://schema.org", > "@type" : "Dataset", > "name" : "Superset" , > "dataset" : { "@type" : "DataSet", > "name" : "Subset" }} > } } > </script> > > Is currently not accepted by the google structured data testing tool. > > Regards, > Jerven > > On 2018-09-24 15:44, Gray, Alasdair J G wrote: >> It would seem that there is no real argument for having DataRecord as >> a separate type from Dataset. All the properties that we need for a >> DataRecord are already in the schema.org/Dataset [8] type. In fact, in >> the specification we even say that a record is a dataset >> >>> A Record acts itself as a dataset although it refers to what could >>> be seen as the minimum compact, complete and auto-descriptive unit >>> in a dataset, i.e., a record. Bioschemas usage In Life Sciences, >>> records will represent a BioChemEntity >> >> Are there any objections to us changing the DataRecord profile to use >> the schema.org/Dataset [8] type and removing the suggestion of a >> DataRecord type? >> >> Alasdair >> >>> On 10 Sep 2018, at 16:31, Shimoyama, Mary <shimoyama@mcw.edu> wrote: >>> >>> >>> Absolutely agree with (b) – the elements on a web page change >>> regularly – for most of the MODs, these can change daily, weekly, >>> monthly. He is right that the elements displayed on a webpage are >>> integrated from queries and present views of data from multiple >>> datasets within the overall structure of the resource. As for (c) on >>> a gene page there are elements that each have unique identifiers >>> >>> FROM: Clark, Timothy W. [mailto:TWCLARK@mgh.harvard.edu] >>> SENT: Monday, September 10, 2018 10:06 AM >>> TO: Rafael Jimenez <rafael.jimenez@elixir-europe.org> >>> CC: Shimoyama, Mary <shimoyama@mcw.edu>; Leyla Garcia >>> <ljgarcia@ebi.ac.uk>; Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>; Dan >>> Brickley <danbri@google.com>; public-bioschemas@w3.org; Natasha Noy >>> <noy@google.com>; Vicki Tardif Holland <vtardif@google.com> >>> SUBJECT: Re: DataRecord and Dataset Search >>> >>> ATTENTION: This email originated from a sender outside of MCW. Use >>> caution when clicking on links or opening attachments. >>> >>> ------------------------- >>> >>> (a) Pointing out that since a set may have cardinality = 1, a data >>> record is certainly a data set. >>> >>> (b) I wonder if using the concept “record” to mean the contents >>> of a web page could be problematic when pages are constructed by >>> queries and views on underlying data resources and assembled not >>> based on normalization rules but for best UX purposes and contain a >>> melange of many elements some of which are repeating. >>> >>> (c) For example, supposing we assign FOO:0010 to identify a web >>> page containing some information, all of which is not in 1st normal >>> form, i.e. it contains some unique attributes and some repeating >>> groups? And those group elements have their own identifiers >>> assigned, e.g FOO:0001, FOO:0002, etc? What are we looking at ? >>> Does FOO:0010 identify a dataset or a data record? >>> >>> (d) But if you stick with dataset “all the way down” you may be >>> better off, FOO:0010, FOO:0001, and FOO:0002 are all datasets. >>> >>> Something to consider. >>> >>> Tim >>> >>> On Sep 10, 2018, at 10:40 AM, Rafael C. Jimenez >>> <rafael.jimenez@elixir-europe.org> wrote: >>> >>> EXTERNAL EMAIL - USE CAUTION >>> >>> To me, a data record could belong to one or more datasets. It >>> depends on the structure and organisation of the data resource. Data >>> records could be organised in datasets in many different ways. For >>> instance, by the species they belong to, the disease they have been >>> classified to (ie. cardiomegaly) or the experiment they were >>> identified in. >>> >>> To give some examples of data records, below some links pointing to >>> different types of data records: >>> >>> - Protein record in UniProt: MAILSCANNER HAS DETECTED A POSSIBLE >>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE >>> http://identifiers.org/uniprot:P69905 [1] >>> >>> - Protein record in PDB: MAILSCANNER HAS DETECTED A POSSIBLE >>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE >>> http://identifiers.org/pdb:4n7n [2] >>> >>> - Chemical record in ChEBI: MAILSCANNER HAS DETECTED A POSSIBLE >>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE >>> http://identifiers.org/CHEBI:27732 [3] >>> >>> - Gene record in ENSEMBL: MAILSCANNER HAS DETECTED A POSSIBLE >>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE >>> http://identifiers.org/ensembl:ENSG00000244734 [4] >>> >>> I like in Bioschmeas we are trying to annotate all our data >>> resources using few types and relationships: DataCatalog -> DataSet >>> -> DataRecord[BioChemEntity]. Some of our data resources like EGA or >>> OmicsDI will have a high number of datasets, but I think the >>> majority of our resources (UniProt, PDB, ChEBI or ENSEMBL mentioned >>> above) will have a high number of data records and few datasets. >>> Sometimes some of our data resources might even have just one >>> dataset for all their data records. >>> >>> The alternative Alasdair is talking about is to use the DataSet >>> type for the concept of DataRecord. It would be to change to >>> DataCatalog -> DataSet -> DataSet[BioChemEntity]. Though for some >>> people it might not be semantically that correct I think this >>> approach has some advantages: 1. We do not need to propose a new >>> type DataRecord type to MAILSCANNER HAS DETECTED A POSSIBLE FRAUD >>> ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE schema.org >>> [5], 2.- The properties we wanted to use for DataRecord are already >>> in the DataSet type, 3.- Our data records will also be displayed in >>> the Google dataset search, 4.- It does not really change much the >>> way we have been working in Bioschemas. >>> >>> Bringing back the question from Alisdair, which I think it is >>> important. Should we push for a new DataRecord type in MAILSCANNER >>> HAS DETECTED A POSSIBLE FRAUD ATTEMPT FROM >>> "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE Schema.org [6] or should >>> we re-use the DataSet type instead? >>> >>> Regards, >>> >>> Rafa >>> >>> On Mon, 10 Sep 2018 at 15:19, Shimoyama, Mary <shimoyama@mcw.edu> >>> wrote: >>> Is there some thought to the idea of a data record belonging to >>> multiple datasets? For example, there is an annotation for the rat >>> A2m gene indicating it is associated with cardiomegaly. Does this >>> A2m-cardiomegaly record belong to the dataset of the A2m gene and >>> all of the data related to A2m, does it belong to the dataset of >>> Cardiomegaly and all of the genes associated with cardiomegaly, does >>> it belong to the dataset of all the annotations and data taken from >>> PMID:12494268/RGDID:1549856, does it belong to the dataset of all >>> rat genes and their disease annotations or does it belong to the >>> dataset of the entire RGD corpus of data? >>> >>> -----Original Message----- >>> From: Clark, Timothy W. [mailto:TWCLARK@mgh.harvard.edu] >>> Sent: Monday, September 10, 2018 8:04 AM >>> To: ljgarcia <ljgarcia@ebi.ac.uk> >>> Cc: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>; Dan Brickley >>> <danbri@google.com>; public-bioschemas@w3.org; Natasha Noy >>> <noy@google.com>; Vicki Tardif Holland <vtardif@google.com>; >>> Shimoyama, Mary <shimoyama@mcw.edu> >>> Subject: Re: DataRecord and Dataset Search >>> >>> ATTENTION: This email originated from a sender outside of MCW. Use >>> caution when clicking on links or opening attachments. >>> ________________________________ >>> >>> Just adding in Mary Shimoyama PI of RGB to this discussion. >>> >>>> On Sep 10, 2018, at 8:35 AM, ljgarcia <ljgarcia@ebi.ac.uk> wrote: >>>> >>>> External Email - Use Caution >>>> Hi Alasdair, >>>> >>>> I sounds to me you have covered it all. Maybe just some more >>> information about how we link sdo:Dataset, bs:DataRecord and >>> bs:BioChemEntity. sdo:Dataset sdo:hasPart bs:DataRecord (DataRecord >>> actually extends from Dataset) and then sdo:DataRecord sdo:isPartOf >>> sdo:Dataset. A sdo:DataRecord has sdo:maiEntity bs:BioChemEntity and >>> then a bs:BioChemEntity is sdo:mainEntityOfPage of a sdo:DataRecord. >>>> >>>> DataRecord include two additional properties: >>>> * sdo:additionalProperty because we want everybody to be able to >>> add >>>> no-named properties as needed >>>> * bs:seeAlso so ther can be links to related data records in other >>> datasets, this one is very important in Life Sciences. >>>> >>>> Note: I am using sdo for MAILSCANNER HAS DETECTED A POSSIBLE FRAUD >>> ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE schema.org >>> [5] and bs for bioschemas, although bioschemas types along with >>> their properties should go to MAILSCANNER HAS DETECTED A POSSIBLE >>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE >>> schema.org [5] at some point (hopefully soon). >>>> >>>> Regards, >>>> >>>> On 2018-09-09 19:03, Gray, Alasdair J G wrote: >>>>> Hi Dan >>>>> In the life sciences datasets, the individual records tend to get >>> >>>>> their own web page, i.e. each concept in the database would have >>> its >>>>> own page. The idea for the DataRecord is to be able declare that >>> the >>>>> page about a concept is part of a Dataset. >>>>> I believe the approach is agnostic to the underlying storage, >>> i.e. >>>>> the page could be generated from a relational database which >>> pulls >>>>> data about the concept from multiple tables, a triplestore, or >>> some >>>>> other form of database. It is more about the granularity of this >>>>> being about a single concept, e.g. row in a relational database >>> with >>>>> its foreign keys. >>>>> Leyla, Rafa, Susanna, what do you think? Have I characterised >>> this >>>>> correctly or are there things in Dan’s email that I am missing. >>>>> Alasdair >>>>>> On 7 Sep 2018, at 18:12, Dan Brickley <danbri@google.com> wrote: >>>>>> (+Natasha Noy, +Vicki Tardif Holland) On Fri, 7 Sep 2018 at >>> 15:54, >>>>>> Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk> wrote: >>>>>>> Hi Dan, >>>>>>> Great to see the announcement this week about the Google >>> Dataset >>>>>>> search. Here is a link to a blog post for anyone who has not >>> seen >>>>>>> it yet >>>>> >>> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.blog.google_ >>>>> >>> >> products_search_making-2Dit-2Deasier-2Ddiscover-2Ddatasets_&d=DwIGaQ& >>>>> >>> >> c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5Tsee >>>>> >>> >> hzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQKLroB0DANNTw2d0tisoNx7KJQZ1xegXqyg& >>>>> s=X7OaasRJiIqJhU4v5NnlNJGHFRGBPnsqrNJMduz-DKQ&e= >>>>>>> Within Bioschemas, we have been building up a profile usage of >>>>>>> DataCatalog containing Dataset(s) which themselves contain >>>>>>> DataRecords. A DataRecord is something that we would be >>> proposing >>>>>>> as an addition to MAILSCANNER HAS DETECTED A POSSIBLE FRAUD >>> ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE schema.org >>> [5] [1]. The idea is that a DataRecord is >>>>>>> contained within a Dataset and would specify the types of >>> entity >>>>>>> that the record is about, e.g. Protein. >>>>>>> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioschemas.org_ >>>>>>> >>> types_DataRecord_specification_&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iq >>>>>>> >>> Fn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m >>>>>>> >>> =9Do_KY8oQKLroB0DANNTw2d0tisoNx7KJQZ1xegXqyg&s=VQXoaBLgxbCy_Qxi4h8R >>>>>>> bqij_biYI-o3xrRcqvYMSPg&e= We would like to understand whether >>>>>>> DataRecord is an idea to which the MAILSCANNER HAS DETECTED A >>> POSSIBLE FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO >>> BE schema.org [5] [1] community would >>>>>>> be receptive. An alternative approach would be to use Dataset >>> for >>>>>>> both records within a Dataset and the Dataset itself. >>>>>> It is certainly a direction worth exploring and discussing. >>>>>> One issue to think through (and I think I raised this at a >>>>>> bioschemas f2f last year) is that "Dataset" is a very broad >>> notion. >>>>>> Some but not all datasets are tabular for example. And tabular >>> (e.g. >>>>>> csv, sql) structures have non-trivial mappings to >>> "entity"-oriented >>>>>> and "record"-oriented representations. Other formats will have >>>>>> different (and possibly simpler) ideas about "records". Thinking >>> >>>>>> about tabular first, there are complex mapping languages like >>> D2RQ >>>>>> or >>>>>> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.w3.org_TR_r >>>>>> >>> >> 2rml_&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQKLroB0DANNTw2d0tisoNx7KJQZ1xegXqyg&s=MYcr4sn8940aywRFbBWENNFVPxseMcirke2j3PEHUcM&e= >> >>> and the RDF graph it generates versus a rows-as-records view, how >>> would your draft design deal with multi-table datasets? >>>>>> Nearby in this world are specs like W3C CSVW, Data Cube, ... >>> lots of >>>>>> overlaps. It would be great to work through some examples in >>>>>> detail... >>>>>> Dan >>>>>>> Thanks >>>>>>> Alasdair >>>>>>> -- >>>>>>> Alasdair J G Gray >>>>>>> Associate Professor in Computer Science, School of Mathematical >>> and >>>>>>> Computer Sciences Heriot-Watt University, Edinburgh, UK. >>>>>>> Email: A.J.G.Gray@hw.ac.uk >>>>>>> Web: >>>>>>> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.macs.hw.ac. >>>>>>> >>> uk_-7Eajg33&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y& >>>>>>> >>> r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQKLroB0DANN >>>>>>> >>> Tw2d0tisoNx7KJQZ1xegXqyg&s=g-Y7L58vpqNcKEE1Av3OwMNwrCN0DZuOoxkll837 >>>>>>> 5ZY&e= >>>>>>> ORCID: >>>>>>> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__orcid.org_0000- >>>>>>> >>> 2D0002-2D5711-2D4872&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ >>>>>>> >>> kjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQK >>>>>>> >>> LroB0DANNTw2d0tisoNx7KJQZ1xegXqyg&s=m2htr8bZ5GnacvnHur2nmU2ZA_whdHa >>>>>>> qMu07RxqWC8o&e= >>>>>>> Office: Earl Mountbatten Building 1.39 >>>>>>> Twitter: @gray_alasdair >>>>>>> ------------------------- >>>>>>> _HERIOT-WATT UNIVERSITY IS THE TIMES & THE SUNDAY TIMES >>>>>>> INTERNATIONAL UNIVERSITY OF THE YEAR 2018_ Founded in 1821, >>>>>>> Heriot-Watt is a leader in ideas and solutions. >>>>>>> With campuses and students across the entire globe we span the >>>>>>> world, delivering innovation and educational excellence in >>>>>>> business, engineering, design and the physical, social and life >>> >>>>>>> sciences. >>>>>>> This email is generated from the Heriot-Watt University Group, >>>>>>> which includes: >>>>>>> * Heriot-Watt University, a Scottish charity registered under >>>>>>> number SC000278 >>>>>>> * Edinburgh Business School a Charity Registered in Scotland, >>>>>>> SC026900. 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If the e-mail was sent to you in error but does not contain >>> patient information, please contact the sender and properly dispose >>> of the e-mail. >>> >>> -- >>> >>> RAFAEL C JIMENEZ >>> >>> ELIXIR Chief Data Architect >>> MAILSCANNER HAS DETECTED A POSSIBLE FRAUD ATTEMPT FROM >>> "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE www.elixir-europe.org [7] >>> >>> >>> ELIXIR Hub, South Building >>> Wellcome Genome Campus >>> Hinxton, Cambridge, CB10 1SD, UK >>> Tel: +44 (0) 1223 49 2574 >>> E-Mail: rafael.jimenez@elixir-europe.org >> >> -- >> Alasdair J G Gray >> Associate Professor in Computer Science, >> School of Mathematical and Computer Sciences >> Heriot-Watt University, Edinburgh, UK. >> >> Email: A.J.G.Gray@hw.ac.uk >> Web: http://www.macs.hw.ac.uk/~ajg33 >> ORCID: http://orcid.org/0000-0002-5711-4872 >> Office: Earl Mountbatten Building 1.39 >> Twitter: @gray_alasdair >> >> >> >> Links: >> ------ >> [1] >> https://urldefense.proofpoint.com/v2/url?u=http-3A__identifiers.org_uniprot-3AP69905&d=DwMGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&s=fcvRDFkHxKmxBT5NqR3zy23AhHgrcqxJhBrr1YQIxbc&e= >> >> [2] >> https://urldefense.proofpoint.com/v2/url?u=http-3A__identifiers.org_pdb-3A4n7n&d=DwMGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&s=6bhzIha2rtBDN1b-UapJW6wNsUDYmlpTTc7RkVIwJGk&e= >> >> [3] >> https://urldefense.proofpoint.com/v2/url?u=http-3A__identifiers.org_CHEBI-3A27732&d=DwMGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&s=3euSTTFX7v7hVnJZ_pNaJt_UyX-pFPSl_lvgBzDh91M&e= >> >> [4] >> https://urldefense.proofpoint.com/v2/url?u=http-3A__identifiers.org_ensembl-3AENSG00000244734&d=DwMGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&s=LOx1vWRdWE3jr5V1dFSg55lp6iGm8dl6NKwu5e0xsnI&e= >> >> [5] >> https://urldefense.proofpoint.com/v2/url?u=http-3A__schema.org_&d=DwMGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&s=pWdXlfBCWDRHFvEWI4bEWwBlqRlBzfaiJY2FFHH0yaM&e= >> >> [6] >> https://urldefense.proofpoint.com/v2/url?u=http-3A__Schema.org&d=DwMGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&s=0dpHewweLhkTKo1BgBEW71rBPWIKeH7QrO3-TDdQ7yI&e= >> >> [7] >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.elixir-2Deurope.org_&d=DwMGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&s=KR4sA_rKQ8wSkfEz0yrQ7flS0WlBByOWK55z8EEX-UQ&e= >> >> [8] http://schema.org/Dataset >
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