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ravila4/BioservicesUniProt.ipynb

Created July 7, 2018 17:37
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Getting UniProt Annotations
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BioservicesUniProt.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Getting UniProt Annotations from Bioservices Module"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from bioservices import UniProt"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"u = UniProt(verbose=False)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Query gene and get sequence"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Entry\n",
"P43403\n",
"\n"
]
}
],
"source": [
"q = u.search(\"ZAP70_HUMAN\", columns=\"id\")\n",
"print(q)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
">sp|P43403|ZAP70_HUMAN Tyrosine-protein kinase ZAP-70 OS=Homo sapiens OX=9606 GN=ZAP70 PE=1 SV=1\n",
"MPDPAAHLPFFYGSISRAEAEEHLKLAGMADGLFLLRQCLRSLGGYVLSLVHDVRFHHFP\n",
"IERQLNGTYAIAGGKAHCGPAELCEFYSRDPDGLPCNLRKPCNRPSGLEPQPGVFDCLRD\n",
"AMVRDYVRQTWKLEGEALEQAIISQAPQVEKLIATTAHERMPWYHSSLTREEAERKLYSG\n",
"AQTDGKFLLRPRKEQGTYALSLIYGKTVYHYLISQDKAGKYCIPEGTKFDTLWQLVEYLK\n",
"LKADGLIYCLKEACPNSSASNASGAAAPTLPAHPSTLTHPQRRIDTLNSDGYTPEPARIT\n",
"SPDKPRPMPMDTSVYESPYSDPEELKDKKLFLKRDNLLIADIELGCGNFGSVRQGVYRMR\n",
"KKQIDVAIKVLKQGTEKADTEEMMREAQIMHQLDNPYIVRLIGVCQAEALMLVMEMAGGG\n",
"PLHKFLVGKREEIPVSNVAELLHQVSMGMKYLEEKNFVHRDLAARNVLLVNRHYAKISDF\n",
"GLSKALGADDSYYTARSAGKWPLKWYAPECINFRKFSSRSDVWSYGVTMWEALSYGQKPY\n",
"KKMKGPEVMAFIEQGKRMECPPECPPELYALMSDCWIYKWEDRPDFLTVEQRMRACYYSL\n",
"ASKVEGPPGSTQKAEAACA\n",
"\n"
]
}
],
"source": [
"fa = u.retrieve(\"P43403\", frmt=\"fasta\")\n",
"print(fa)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get UniProt dataframe"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Entry</th>\n",
" <th>Entry name</th>\n",
" <th>Gene names</th>\n",
" <th>Gene names (primary )</th>\n",
" <th>Gene names (synonym )</th>\n",
" <th>Gene names (ordered locus )</th>\n",
" <th>Gene names (ORF )</th>\n",
" <th>Organism</th>\n",
" <th>Organism ID</th>\n",
" <th>Protein names</th>\n",
" <th>...</th>\n",
" <th>Taxonomic lineage IDs (GENUS)</th>\n",
" <th>Taxonomic lineage IDs (SUBGENUS)</th>\n",
" <th>Taxonomic lineage IDs (SPECIES GROUP)</th>\n",
" <th>Taxonomic lineage IDs (SPECIES SUBGROUP)</th>\n",
" <th>Taxonomic lineage IDs (SPECIES)</th>\n",
" <th>Taxonomic lineage IDs (SUBSPECIES)</th>\n",
" <th>Taxonomic lineage IDs (VARIETAS)</th>\n",
" <th>Taxonomic lineage IDs (FORMA)</th>\n",
" <th>Cross-reference (db_abbrev)</th>\n",
" <th>Cross-reference (EMBL)</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>P43403</td>\n",
" <td>ZAP70_HUMAN</td>\n",
" <td>[ZAP70 SRK]</td>\n",
" <td>ZAP70</td>\n",
" <td>SRK</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>Homo sapiens (Human)</td>\n",
" <td>9606</td>\n",
" <td>Tyrosine-protein kinase ZAP-70 (EC 2.7.10.2) (...</td>\n",
" <td>...</td>\n",
" <td>9605</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>AB083211;AC016699;BC039039;BC053878;</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>F9XDX0</td>\n",
" <td>F9XDX0_ZYMTI</td>\n",
" <td>[MYCGRDRAFT_43403]</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>MYCGRDRAFT_43403</td>\n",
" <td>Zymoseptoria tritici (strain CBS 115943 / IPO3...</td>\n",
" <td>336722</td>\n",
" <td>DNA helicase (EC 3.6.4.12)</td>\n",
" <td>...</td>\n",
" <td>1047167</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>1047171.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>CM001201;</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>2 rows × 178 columns</p>\n",
"</div>"
],
"text/plain": [
" Entry Entry name Gene names Gene names (primary ) \\\n",
"0 P43403 ZAP70_HUMAN [ZAP70 SRK] ZAP70 \n",
"1 F9XDX0 F9XDX0_ZYMTI [MYCGRDRAFT_43403] NaN \n",
"\n",
" Gene names (synonym ) Gene names (ordered locus ) Gene names (ORF ) \\\n",
"0 SRK NaN NaN \n",
"1 NaN NaN MYCGRDRAFT_43403 \n",
"\n",
" Organism Organism ID \\\n",
"0 Homo sapiens (Human) 9606 \n",
"1 Zymoseptoria tritici (strain CBS 115943 / IPO3... 336722 \n",
"\n",
" Protein names \\\n",
"0 Tyrosine-protein kinase ZAP-70 (EC 2.7.10.2) (... \n",
"1 DNA helicase (EC 3.6.4.12) \n",
"\n",
" ... Taxonomic lineage IDs (GENUS) \\\n",
"0 ... 9605 \n",
"1 ... 1047167 \n",
"\n",
" Taxonomic lineage IDs (SUBGENUS) Taxonomic lineage IDs (SPECIES GROUP) \\\n",
"0 NaN NaN \n",
"1 NaN NaN \n",
"\n",
" Taxonomic lineage IDs (SPECIES SUBGROUP) Taxonomic lineage IDs (SPECIES) \\\n",
"0 NaN NaN \n",
"1 NaN 1047171.0 \n",
"\n",
" Taxonomic lineage IDs (SUBSPECIES) Taxonomic lineage IDs (VARIETAS) \\\n",
"0 NaN NaN \n",
"1 NaN NaN \n",
"\n",
" Taxonomic lineage IDs (FORMA) Cross-reference (db_abbrev) \\\n",
"0 NaN NaN \n",
"1 NaN NaN \n",
"\n",
" Cross-reference (EMBL) \n",
"0 AB083211;AC016699;BC039039;BC053878; \n",
"1 CM001201; \n",
"\n",
"[2 rows x 178 columns]"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df = u.get_df(['P43403'], nChunk=100, organism=None)\n",
"df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Available fields:"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['Entry',\n",
" 'Entry name',\n",
" 'Gene names',\n",
" 'Gene names (primary )',\n",
" 'Gene names (synonym )',\n",
" 'Gene names (ordered locus )',\n",
" 'Gene names (ORF )',\n",
" 'Organism',\n",
" 'Organism ID',\n",
" 'Protein names',\n",
" 'Proteomes',\n",
" 'Taxonomic lineage (ALL)',\n",
" 'Taxonomic lineage IDs',\n",
" 'Virus hosts',\n",
" 'Sequence',\n",
" 'Length',\n",
" 'Mass',\n",
" 'Gene encoded by',\n",
" 'Alternative products (isoforms)',\n",
" 'Erroneous gene model prediction',\n",
" 'Erroneous initiation',\n",
" 'Erroneous termination',\n",
" 'Erroneous translation',\n",
" 'Frameshift',\n",
" 'Mass spectrometry',\n",
" 'Polymorphism',\n",
" 'RNA editing',\n",
" 'Sequence caution',\n",
" 'Alternative sequence',\n",
" 'Natural variant',\n",
" 'Non-adjacent residues',\n",
" 'Non-standard residue',\n",
" 'Non-terminal residue',\n",
" 'Sequence conflict',\n",
" 'Sequence uncertainty',\n",
" 'Version (sequence)',\n",
" 'Domains',\n",
" 'Domain count',\n",
" 'Domain [CC]',\n",
" 'Sequence similarities',\n",
" 'Coiled coil',\n",
" 'Compositional bias',\n",
" 'Domain [FT]',\n",
" 'Motif',\n",
" 'Region',\n",
" 'Repeat',\n",
" 'Zinc finger',\n",
" 'EC number',\n",
" 'Absorption',\n",
" 'Catalytic activity',\n",
" 'Cofactor',\n",
" 'Enzyme regulation',\n",
" 'Function [CC]',\n",
" 'Kinetics',\n",
" 'Pathway',\n",
" 'Redox potential',\n",
" 'Temperature dependence',\n",
" 'pH dependence',\n",
" 'Active site',\n",
" 'Binding site',\n",
" 'DNA binding',\n",
" 'Metal binding',\n",
" 'Nucleotide binding',\n",
" 'Site',\n",
" 'Gene ontology (GO)',\n",
" 'Gene ontology (biological process)',\n",
" 'Gene ontology (molecular function)',\n",
" 'Gene ontology (cellular component)',\n",
" 'Gene ontology IDs',\n",
" 'InterPro',\n",
" 'Interacts with',\n",
" 'Subunit structure [CC]',\n",
" 'PubMed ID',\n",
" 'Mapped PubMed ID',\n",
" 'Date of creation',\n",
" 'Date of last modification',\n",
" 'Date of last sequence modification',\n",
" 'Version (entry)',\n",
" '3D',\n",
" 'Beta strand',\n",
" 'Helix',\n",
" 'Turn',\n",
" 'Subcellular location [CC]',\n",
" 'Intramembrane',\n",
" 'Topological domain',\n",
" 'Transmembrane',\n",
" 'Annotation',\n",
" 'Features',\n",
" 'Caution',\n",
" 'Tissue specificity',\n",
" 'Miscellaneous [CC]',\n",
" 'Keywords',\n",
" 'Protein existence',\n",
" 'Status',\n",
" 'Sequence annotation (Features)',\n",
" 'Protein families',\n",
" 'Version',\n",
" 'Comments',\n",
" 'Cross-reference (null)',\n",
" 'Pathway.1',\n",
" 'Allergenic properties',\n",
" 'Biotechnological use',\n",
" 'Disruption phenotype',\n",
" 'Involvement in disease',\n",
" 'Pharmaceutical use',\n",
" 'Toxic dose',\n",
" 'Post-translational modification',\n",
" 'Chain',\n",
" 'Cross-link',\n",
" 'Disulfide bond',\n",
" 'Glycosylation',\n",
" 'Initiator methionine',\n",
" 'Lipidation',\n",
" 'Modified residue',\n",
" 'Peptide',\n",
" 'Propeptide',\n",
" 'Signal peptide',\n",
" 'Transit peptide',\n",
" 'Taxonomic lineage (all)',\n",
" 'Taxonomic lineage (SUPERKINGDOM)',\n",
" 'Taxonomic lineage (KINGDOM)',\n",
" 'Taxonomic lineage (SUBKINGDOM)',\n",
" 'Taxonomic lineage (SUPERPHYLUM)',\n",
" 'Taxonomic lineage (PHYLUM)',\n",
" 'Taxonomic lineage (SUBPHYLUM)',\n",
" 'Taxonomic lineage (SUPERCLASS)',\n",
" 'Taxonomic lineage (CLASS)',\n",
" 'Taxonomic lineage (SUBCLASS)',\n",
" 'Taxonomic lineage (INFRACLASS)',\n",
" 'Taxonomic lineage (SUPERORDER)',\n",
" 'Taxonomic lineage (ORDER)',\n",
" 'Taxonomic lineage (SUBORDER)',\n",
" 'Taxonomic lineage (INFRAORDER)',\n",
" 'Taxonomic lineage (PARVORDER)',\n",
" 'Taxonomic lineage (SUPERFAMILY)',\n",
" 'Taxonomic lineage (FAMILY)',\n",
" 'Taxonomic lineage (SUBFAMILY)',\n",
" 'Taxonomic lineage (TRIBE)',\n",
" 'Taxonomic lineage (SUBTRIBE)',\n",
" 'Taxonomic lineage (GENUS)',\n",
" 'Taxonomic lineage (SUBGENUS)',\n",
" 'Taxonomic lineage (SPECIES GROUP)',\n",
" 'Taxonomic lineage (SPECIES SUBGROUP)',\n",
" 'Taxonomic lineage (SPECIES)',\n",
" 'Taxonomic lineage (SUBSPECIES)',\n",
" 'Taxonomic lineage (VARIETAS)',\n",
" 'Taxonomic lineage (FORMA)',\n",
" 'Taxonomic lineage IDs (all)',\n",
" 'Taxonomic lineage IDs (SUPERKINGDOM)',\n",
" 'Taxonomic lineage IDs (KINGDOM)',\n",
" 'Taxonomic lineage IDs (SUBKINGDOM)',\n",
" 'Taxonomic lineage IDs (SUPERPHYLUM)',\n",
" 'Taxonomic lineage IDs (PHYLUM)',\n",
" 'Taxonomic lineage IDs (SUBPHYLUM)',\n",
" 'Taxonomic lineage IDs (SUPERCLASS)',\n",
" 'Taxonomic lineage IDs (CLASS)',\n",
" 'Taxonomic lineage IDs (SUBCLASS)',\n",
" 'Taxonomic lineage IDs (INFRACLASS)',\n",
" 'Taxonomic lineage IDs (SUPERORDER)',\n",
" 'Taxonomic lineage IDs (ORDER)',\n",
" 'Taxonomic lineage IDs (SUBORDER)',\n",
" 'Taxonomic lineage IDs (INFRAORDER)',\n",
" 'Taxonomic lineage IDs (PARVORDER)',\n",
" 'Taxonomic lineage IDs (SUPERFAMILY)',\n",
" 'Taxonomic lineage IDs (FAMILY)',\n",
" 'Taxonomic lineage IDs (SUBFAMILY)',\n",
" 'Taxonomic lineage IDs (TRIBE)',\n",
" 'Taxonomic lineage IDs (SUBTRIBE)',\n",
" 'Taxonomic lineage IDs (GENUS)',\n",
" 'Taxonomic lineage IDs (SUBGENUS)',\n",
" 'Taxonomic lineage IDs (SPECIES GROUP)',\n",
" 'Taxonomic lineage IDs (SPECIES SUBGROUP)',\n",
" 'Taxonomic lineage IDs (SPECIES)',\n",
" 'Taxonomic lineage IDs (SUBSPECIES)',\n",
" 'Taxonomic lineage IDs (VARIETAS)',\n",
" 'Taxonomic lineage IDs (FORMA)',\n",
" 'Cross-reference (db_abbrev)',\n",
" 'Cross-reference (EMBL)']"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"list(df.keys())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Example queries"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'FUNCTION: Tyrosine kinase that plays an essential role in regulation of the adaptive immune response. Regulates motility, adhesion and cytokine expression of mature T-cells, as well as thymocyte development. Contributes also to the development and activation of primary B-lymphocytes. When antigen presenting cells (APC) activate T-cell receptor (TCR), a serie of phosphorylations lead to the recruitment of ZAP70 to the doubly phosphorylated TCR component CD247/CD3Z through ITAM motif at the plasma membrane. This recruitment serves to localization to the stimulated TCR and to relieve its autoinhibited conformation. Release of ZAP70 active conformation is further stabilized by phosphorylation mediated by LCK. Subsequently, ZAP70 phosphorylates at least 2 essential adapter proteins: LAT and LCP2. In turn, a large number of signaling molecules are recruited and ultimately lead to lymphokine production, T-cell proliferation and differentiation. Furthermore, ZAP70 controls cytoskeleton modifications, adhesion and mobility of T-lymphocytes, thus ensuring correct delivery of effectors to the APC. ZAP70 is also required for TCR-CD247/CD3Z internalization and degradation through interaction with the E3 ubiquitin-protein ligase CBL and adapter proteins SLA and SLA2. Thus, ZAP70 regulates both T-cell activation switch on and switch off by modulating TCR expression at the T-cell surface. During thymocyte development, ZAP70 promotes survival and cell-cycle progression of developing thymocytes before positive selection (when cells are still CD4/CD8 double negative). Additionally, ZAP70-dependent signaling pathway may also contribute to primary B-cells formation and activation through B-cell receptor (BCR). {ECO:0000269|PubMed:11353765, ECO:0000269|PubMed:12051764, ECO:0000269|PubMed:1423621, ECO:0000269|PubMed:20135127, ECO:0000269|PubMed:26903241, ECO:0000269|PubMed:8124727, ECO:0000269|PubMed:8702662, ECO:0000269|PubMed:9489702}.'"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df['Function [CC]'][0]"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'CATALYTIC ACTIVITY: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate. {ECO:0000255|PROSITE-ProRule:PRU10028, ECO:0000269|PubMed:15292186}.'"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df['Catalytic activity'][0]"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'ACT_SITE 461 461 Proton acceptor. {ECO:0000255|PROSITE-ProRule:PRU00159, ECO:0000255|PROSITE-ProRule:PRU10028, ECO:0000269|PubMed:15292186, ECO:0000269|PubMed:17512407}.'"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df['Active site'][0]"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'BINDING 369 369 ATP.'"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df['Binding site'][0]"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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