A relational database for sequence-specific protein NMR data View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1991-09

AUTHORS

Beverly R. Seavey, Elizabeth A. Farr, William M. Westler, John L. Markley

ABSTRACT

A protein NMR database has been designed and is being implemented. The database is intended to contain solution NMR results from proteins and peptides (larger than 12 residues). A relational database format has been chosen that indexes data by: primary journal citation, molecular species, sequence-related and atom-specific assignments, and experimental conditions. At present, all data are entered from the primary refereed literature. Examples are given of sample queries to the database. Possible distribution formats are discussed. More... »

PAGES

217-236

References to SciGraph publications

  • 1983. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) in NUCLEIC ACIDS: THE VECTORS OF LIFE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/bf01875516

    DOI

    http://dx.doi.org/10.1007/bf01875516

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1033409469

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/1841696


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biochemistry and Cell Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Animals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Databases, Bibliographic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Magnetic Resonance Spectroscopy", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Peptides", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Protein Conformation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Proteins", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA", 
              "id": "http://www.grid.ac/institutes/grid.14003.36", 
              "name": [
                "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA", 
                "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Seavey", 
            "givenName": "Beverly R.", 
            "id": "sg:person.0620066600.21", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0620066600.21"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA", 
              "id": "http://www.grid.ac/institutes/grid.14003.36", 
              "name": [
                "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA", 
                "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Farr", 
            "givenName": "Elizabeth A.", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA", 
              "id": "http://www.grid.ac/institutes/grid.14003.36", 
              "name": [
                "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Westler", 
            "givenName": "William M.", 
            "id": "sg:person.0747237014.02", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0747237014.02"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA", 
              "id": "http://www.grid.ac/institutes/grid.14003.36", 
              "name": [
                "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA", 
                "Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Markley", 
            "givenName": "John L.", 
            "id": "sg:person.0721445644.18", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0721445644.18"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/978-94-009-7225-4_43", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027025514", 
              "https://doi.org/10.1007/978-94-009-7225-4_43"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "1991-09", 
        "datePublishedReg": "1991-09-01", 
        "description": "A protein NMR database has been designed and is being implemented. The database is intended to contain solution NMR results from proteins and peptides (larger than 12 residues). A relational database format has been chosen that indexes data by: primary journal citation, molecular species, sequence-related and atom-specific assignments, and experimental conditions. At present, all data are entered from the primary refereed literature. Examples are given of sample queries to the database. Possible distribution formats are discussed.", 
        "genre": "article", 
        "id": "sg:pub.10.1007/bf01875516", 
        "inLanguage": "en", 
        "isAccessibleForFree": false, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2545308", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2439867", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1101518", 
            "issn": [
              "0925-2738", 
              "1573-5001"
            ], 
            "name": "Journal of Biomolecular NMR", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "3", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "1"
          }
        ], 
        "keywords": [
          "solution NMR results", 
          "protein NMR data", 
          "molecular species", 
          "species", 
          "protein", 
          "NMR data", 
          "peptides", 
          "NMR database", 
          "NMR results", 
          "experimental conditions", 
          "database", 
          "data", 
          "database format", 
          "relational database format", 
          "conditions", 
          "assignment", 
          "results", 
          "example", 
          "relational database", 
          "format", 
          "sample queries", 
          "literature", 
          "citations", 
          "queries", 
          "distribution format", 
          "journal citations", 
          "protein NMR database", 
          "primary journal citation", 
          "atom-specific assignments", 
          "Possible distribution formats", 
          "sequence-specific protein NMR data"
        ], 
        "name": "A relational database for sequence-specific protein NMR data", 
        "pagination": "217-236", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1033409469"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/bf01875516"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "1841696"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/bf01875516", 
          "https://app.dimensions.ai/details/publication/pub.1033409469"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2021-11-01T17:59", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_225.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1007/bf01875516"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/bf01875516'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/bf01875516'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/bf01875516'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/bf01875516'


     

    This table displays all metadata directly associated to this object as RDF triples.

    145 TRIPLES      22 PREDICATES      65 URIs      56 LITERALS      13 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/bf01875516 schema:about N4bd5bc603ed94f639c28b9bcfae03012
    2 Nc75f9fc4e8ea4391bc10a9846692b8e8
    3 Ncae508a1bc834733af08c83bc19f1f45
    4 Ndea447c73908495bbd1a038941f581ab
    5 Nef35a3499cd2446dac7c9f79f034b9eb
    6 Nf5305de62dd94c79ab750a58e1e79a4d
    7 anzsrc-for:06
    8 anzsrc-for:0601
    9 schema:author N77a56e66c74d4286a44f50bf978d19d8
    10 schema:citation sg:pub.10.1007/978-94-009-7225-4_43
    11 schema:datePublished 1991-09
    12 schema:datePublishedReg 1991-09-01
    13 schema:description A protein NMR database has been designed and is being implemented. The database is intended to contain solution NMR results from proteins and peptides (larger than 12 residues). A relational database format has been chosen that indexes data by: primary journal citation, molecular species, sequence-related and atom-specific assignments, and experimental conditions. At present, all data are entered from the primary refereed literature. Examples are given of sample queries to the database. Possible distribution formats are discussed.
    14 schema:genre article
    15 schema:inLanguage en
    16 schema:isAccessibleForFree false
    17 schema:isPartOf N446b758687034964bafa6f1f19f2663d
    18 Ne21d18698ba04e04a2182065ce0cb086
    19 sg:journal.1101518
    20 schema:keywords NMR data
    21 NMR database
    22 NMR results
    23 Possible distribution formats
    24 assignment
    25 atom-specific assignments
    26 citations
    27 conditions
    28 data
    29 database
    30 database format
    31 distribution format
    32 example
    33 experimental conditions
    34 format
    35 journal citations
    36 literature
    37 molecular species
    38 peptides
    39 primary journal citation
    40 protein
    41 protein NMR data
    42 protein NMR database
    43 queries
    44 relational database
    45 relational database format
    46 results
    47 sample queries
    48 sequence-specific protein NMR data
    49 solution NMR results
    50 species
    51 schema:name A relational database for sequence-specific protein NMR data
    52 schema:pagination 217-236
    53 schema:productId N0a95b547f1d142f4861a52e0767b0c33
    54 N356a6db8634245518692ef020625f4ea
    55 Nbb483325898c4487bede688e1e72d3ad
    56 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033409469
    57 https://doi.org/10.1007/bf01875516
    58 schema:sdDatePublished 2021-11-01T17:59
    59 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    60 schema:sdPublisher N23d5cbcbf19e43bd9806b6f34321c1a6
    61 schema:url https://doi.org/10.1007/bf01875516
    62 sgo:license sg:explorer/license/
    63 sgo:sdDataset articles
    64 rdf:type schema:ScholarlyArticle
    65 N082edb72798748068ed09c3589ecb84f rdf:first Nf5a07509577d481e8d888cef933f2a5e
    66 rdf:rest N6c38e2b4d26c4d68945ae585a72478fe
    67 N0a95b547f1d142f4861a52e0767b0c33 schema:name dimensions_id
    68 schema:value pub.1033409469
    69 rdf:type schema:PropertyValue
    70 N23d5cbcbf19e43bd9806b6f34321c1a6 schema:name Springer Nature - SN SciGraph project
    71 rdf:type schema:Organization
    72 N356a6db8634245518692ef020625f4ea schema:name doi
    73 schema:value 10.1007/bf01875516
    74 rdf:type schema:PropertyValue
    75 N446b758687034964bafa6f1f19f2663d schema:volumeNumber 1
    76 rdf:type schema:PublicationVolume
    77 N4b7608fe74e64cc5ba4b0db9af5f159e rdf:first sg:person.0721445644.18
    78 rdf:rest rdf:nil
    79 N4bd5bc603ed94f639c28b9bcfae03012 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    80 schema:name Animals
    81 rdf:type schema:DefinedTerm
    82 N6c38e2b4d26c4d68945ae585a72478fe rdf:first sg:person.0747237014.02
    83 rdf:rest N4b7608fe74e64cc5ba4b0db9af5f159e
    84 N77a56e66c74d4286a44f50bf978d19d8 rdf:first sg:person.0620066600.21
    85 rdf:rest N082edb72798748068ed09c3589ecb84f
    86 Nbb483325898c4487bede688e1e72d3ad schema:name pubmed_id
    87 schema:value 1841696
    88 rdf:type schema:PropertyValue
    89 Nc75f9fc4e8ea4391bc10a9846692b8e8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    90 schema:name Peptides
    91 rdf:type schema:DefinedTerm
    92 Ncae508a1bc834733af08c83bc19f1f45 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    93 schema:name Protein Conformation
    94 rdf:type schema:DefinedTerm
    95 Ndea447c73908495bbd1a038941f581ab schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    96 schema:name Databases, Bibliographic
    97 rdf:type schema:DefinedTerm
    98 Ne21d18698ba04e04a2182065ce0cb086 schema:issueNumber 3
    99 rdf:type schema:PublicationIssue
    100 Nef35a3499cd2446dac7c9f79f034b9eb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    101 schema:name Magnetic Resonance Spectroscopy
    102 rdf:type schema:DefinedTerm
    103 Nf5305de62dd94c79ab750a58e1e79a4d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    104 schema:name Proteins
    105 rdf:type schema:DefinedTerm
    106 Nf5a07509577d481e8d888cef933f2a5e schema:affiliation grid-institutes:grid.14003.36
    107 schema:familyName Farr
    108 schema:givenName Elizabeth A.
    109 rdf:type schema:Person
    110 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    111 schema:name Biological Sciences
    112 rdf:type schema:DefinedTerm
    113 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    114 schema:name Biochemistry and Cell Biology
    115 rdf:type schema:DefinedTerm
    116 sg:grant.2439867 http://pending.schema.org/fundedItem sg:pub.10.1007/bf01875516
    117 rdf:type schema:MonetaryGrant
    118 sg:grant.2545308 http://pending.schema.org/fundedItem sg:pub.10.1007/bf01875516
    119 rdf:type schema:MonetaryGrant
    120 sg:journal.1101518 schema:issn 0925-2738
    121 1573-5001
    122 schema:name Journal of Biomolecular NMR
    123 schema:publisher Springer Nature
    124 rdf:type schema:Periodical
    125 sg:person.0620066600.21 schema:affiliation grid-institutes:grid.14003.36
    126 schema:familyName Seavey
    127 schema:givenName Beverly R.
    128 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0620066600.21
    129 rdf:type schema:Person
    130 sg:person.0721445644.18 schema:affiliation grid-institutes:grid.14003.36
    131 schema:familyName Markley
    132 schema:givenName John L.
    133 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0721445644.18
    134 rdf:type schema:Person
    135 sg:person.0747237014.02 schema:affiliation grid-institutes:grid.14003.36
    136 schema:familyName Westler
    137 schema:givenName William M.
    138 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0747237014.02
    139 rdf:type schema:Person
    140 sg:pub.10.1007/978-94-009-7225-4_43 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027025514
    141 https://doi.org/10.1007/978-94-009-7225-4_43
    142 rdf:type schema:CreativeWork
    143 grid-institutes:grid.14003.36 schema:alternateName Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA
    144 schema:name Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, 53706-1569, Madison, WI, USA
    145 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...