{ "bcoid": "GLY_000574", "title": "Rat Proteoform Citations (Literature Mining)", "description": "The dataset provides citation details corresponding to the PubMed ID (PMID) from file https://data.glygen.org/GLYDS000481. ...", "filename": "rat_proteoform_citations_glycosylation_literature_mining.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Proteoform", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "O35433-1...", "..." ], [ "P09951-1...", "..." ] ], "headers": [ "uniprotkb_ca...", "glytoucan_ac..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glytoucan_ac" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "O35433-1", "", "Characterization of rat transient receptor potential vanilloid 1 receptors lacking the N-glycosylation site N604.", "Neuroreport", "2005 Jun 21", "Wirkner K, Hognestad H, Jahnel R, Hucho F, Illes P", "protein_xref_pubmed", "15931076", "protein_xref_automatic_literature_mining", "15931076" ], [ "P09951-1", "", "Glycosylation sites flank phosphorylation sites on synapsin I: O-linked N-acetylglucosamine residues are localized within domains mediating synapsin I interactions.", "Journal of neurochemistry", "1999 Jul", "Cole RN, Hart GW", "protein_xref_pubmed", "10386995", "protein_xref_automatic_literature_mining", "10386995" ], [ "P09951-1", "", "O-linked beta-N-acetylglucosamine (O-GlcNAc) site thr-87 regulates synapsin I localization to synapses and size of the reserve pool of synaptic vesicles.", "The Journal of biological chemistry", "2014 Feb 7", "Skorobogatko Y, Landicho A, Chalkley RJ, Kossenkov AV, Gallo G, Vosseller K", "protein_xref_pubmed", "24280219", "protein_xref_automatic_literature_mining", "24280219" ], [ "P14740-1", "", "Domain-specific N-glycosylation of the membrane glycoprotein dipeptidylpeptidase IV (CD26) influences its subcellular trafficking, biological stability, enzyme activity and protein folding.", "European journal of biochemistry", "1997 May 15", "Fan H, Meng W, Kilian C, Grams S, Reutter W", "protein_xref_pubmed", "9210490", "protein_xref_automatic_literature_mining", "9210490" ], [ "P14925-1", "", "Topological switching of the COOH-terminal domain of peptidylglycine alpha-amidating monooxygenase by alternative RNA splicing.", "Archives of biochemistry and biophysics", "1993 Feb 15", "Yun HY, Johnson RC, Mains RE, Eipper BA", "protein_xref_pubmed", "7680192", "protein_xref_automatic_literature_mining", "7680192" ], [ "P19493-1", "", "Characterization of the functional role of the N-glycans in the AMPA receptor ligand-binding domain.", "Journal of neurochemistry", "2003 Mar", "Pasternack A, Coleman SK, Fethiere J, Madden DR, LeCaer JP, Rossier J, Pasternack M, Keinanen K", "protein_xref_pubmed", "12603841", "protein_xref_automatic_literature_mining", "12603841" ], [ "P48199-1", "", "Derivation of the amino acid sequence of rat C-reactive protein from cDNA cloning with additional studies on the nature of its dimeric component.", "The Journal of biological chemistry", "1992 Feb 15", "Rassouli M, Sambasivam H, Azadi P, Dell A, Morris HR, Nagpurkar A, Mookerjea S, Murray RK", "protein_xref_pubmed", "1737750", "protein_xref_automatic_literature_mining", "1737750" ], [ "Q05140-1", "", "A novel post-translational modification in nerve terminals: O-linked N-acetylglucosamine phosphorylation.", "Journal of proteome research", "2011 Jun 3", "Graham ME, Thaysen-Andersen M, Bache N, Craft GE, Larsen MR, Packer NH, Robinson PJ", "protein_xref_pubmed", "21500857", "protein_xref_automatic_literature_mining", "21500857" ] ] }, "readme": "Name\n - Rat Proteoform Citations (Literature Mining)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2021-06-04T10:25:25.298469\n\nModified on\n - 2021-06-04T10:27:27.491930\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The dataset provides citation details corresponding to the PubMed ID (PMID) from file https://data.glygen.org/GLYDS000481. The script accesses the NCBI ENTREZ infrastructure to retrieve the publication information of the given PMID.\n\nDescription Domain\n Keywords\n - PMID\n - journal\n - citations\n - authors\n - Literature\n - PubMed\n\n Pipeline Steps\n - Step-1: The script parses the input file for PMIDs and accesses the NCBI Entrez infrastructure to download the publication information of the corresponding PMIDs.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-proteoform-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: rat_proteoform_glycosylation_sites_literature_mining.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/rat_proteoform_glycosylation_sites_literature_mining.csv\n Output Subdomain\n Name: rat_proteoform_citations_glycosylation_literature_mining.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/rat_proteoform_citations_glycosylation_literature_mining.csv\n Name: rat_proteoform_citations_glycosylation_literature_mining.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/rat_proteoform_citations_glycosylation_literature_mining.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/rat_proteoform_citations_glycosylation_literature_mining.csv" }