Bgee annotator

src/pyBiodatafuse/annotators/bgee.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""Python file for queriying Bgee database (https://bgee.org) via its SPARQL endpoint (https://www.bgee.org/sparql/)."""
+
+import datetime
+import os
+from string import Template
+
+import pandas as pd
+from SPARQLWrapper import JSON, SPARQLWrapper
+
+from pyBiodatafuse.utils import collapse_data_sources, get_identifier_of_interest
+
+
+def get_version_bgee() -> dict:
+    """Get version of Bgee RDF data from its SPARQL endpoint.
+
+    # not sure if a version per-se can be retrieved, but the endpoint supports
+    # http://purl.org/dc/terms/modified
+    :returns: a dictionary containing the last modified date information
+    """
+    with open(os.path.dirname(__file__) + "/queries/bgee-get-last-modified.rq", "r") as fin:
+        sparql_query = fin.read()
+
+    sparql = SPARQLWrapper("https://www.bgee.org/sparql/")
+    sparql.setReturnFormat(JSON)
+
+    sparql.setQuery(sparql_query)
+    res = sparql.queryAndConvert()
+
+    bgee_version = {"bgee_version": res["results"]["bindings"][0]["dateModified"]["value"]}
+
+    return bgee_version
+
+
+def get_gene_literature(bridgedb_df: pd.DataFrame, anatomical_entities: pd.DataFrame):
+    """Query gene-tissue expression information from Bgee.
+
+    :param bridgedb_df: BridgeDb output for creating the list of gene ids to query
+    :param anatomical_entities: a dataframe containing the names of Anatomical entities of interest
+    :returns: a DataFrame containing the Bgee output and dictionary of the Bgee metadata.
+    """
+    # Record the start time
+    start_time = datetime.datetime.now()
+
+    data_df = get_identifier_of_interest(bridgedb_df, "Ensembl")
+    gene_list = data_df["target"].tolist()
+    gene_list = list(set(gene_list))
+
+    query_gene_lists = []
+    if len(gene_list) > 25:
+        for i in range(0, len(gene_list), 25):
+            tmp_list = gene_list[i : i + 25]
+            query_gene_lists.append(" ".join(f'"{g}"' for g in tmp_list))
+
+    else:
+        query_gene_lists.append(" ".join(f'"{g}"' for g in gene_list))
+
+    anat_entities_list = anatomical_entities["AnatomicalEntityNames"].tolist()
+    anat_entities_list = list(set(anat_entities_list))
+
+    query_anat_entities_lists = []
+    if len(anat_entities_list) > 25:
+        for i in range(0, len(anat_entities_list), 25):
+            tmp_list = anat_entities_list[i : i + 25]
+            query_anat_entities_lists.append(" ".join(f'"{g}"' for g in tmp_list))
+
+    else:
+        query_anat_entities_lists.append(" ".join(f'"{g}"' for g in anat_entities_list))
+
+    with open(os.path.dirname(__file__) + "/queries/bgee-genes-tissues-expression.rq", "r") as fin:
+        sparql_query = fin.read()
+
+    sparql = SPARQLWrapper("https://www.bgee.org/sparql/")
+    sparql.setReturnFormat(JSON)
+
+    query_count = 0
+
+    results_df_list = list()
+
+    for gene_list_str in query_gene_lists:
+        for query_anat_entities_str in query_anat_entities_lists:
+            query_count += 1
+
+            sparql_query_template = Template(sparql_query)
+            substit_dict = dict(gene_list=gene_list_str, anat_entities_list=query_anat_entities_str)
+            sparql_query_template_sub = sparql_query_template.substitute(substit_dict)
+
+            sparql.setQuery(sparql_query_template_sub)
+            res = sparql.queryAndConvert()
+
+            df = pd.DataFrame(res["results"]["bindings"])
+            df = df.applymap(lambda x: x["value"])
+
+            results_df_list.append(df)
+
+    # Organize the annotation results as an array of dictionaries
+    intermediate_df = pd.concat(results_df_list)
+
+    intermediate_df.rename(columns={"ensemblId": "target"}, inplace=True)
+
+    # Record the end time
+    end_time = datetime.datetime.now()
+
+    # Metadata details
+    # Get the current date and time
+    current_date = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
+
+    # Calculate the time elapsed
+    time_elapsed = str(end_time - start_time)
+
+    # Add version to metadata file
+    bgee_version = get_version_bgee()
+
+    # Add the datasource, query, query time, and the date to metadata
+    bgee_metadata = {
+        "datasource": "Bgee",
+        "metadata": {"source_version": bgee_version},
+        "query": {
+            "size": len(gene_list),
+            "time": time_elapsed,
+            "date": current_date,
+            "url": "https://www.bgee.org/sparql/",
+        },
+    }
+
+    # Merge the two DataFrames on the target column
+    merged_df = collapse_data_sources(
+        data_df=data_df,
+        source_namespace="Ensembl",
+        target_df=intermediate_df,
+        common_cols=["target"],
+        target_specific_cols=[
+            "anatomicalEntity",
+            "anatomicalEntityName",
+            "expressionLevel",
+            "confidenceLevel",
+        ],
+        col_name="Bgee",
+    )
+
+    return merged_df, bgee_metadata

src/pyBiodatafuse/annotators/queries/bgee-genes-tissues-expression.rq

@@ -0,0 +1,25 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX orth: <http://purl.org/net/orth#>
+PREFIX lscr: <http://purl.org/lscr#>
+PREFIX genex: <http://purl.org/genex#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT ?gene ?ensemblId ?geneId ?anatomicalEntity ?anatomicalEntityName ?expressionLevel ?confidenceLevel
+WHERE {
+  VALUES ?ensemblId { $gene_list }
+  VALUES ?anatomicalEntityName { $anat_entities_list }
+  BIND(CONCAT("http://rdf.ebi.ac.uk/resource/ensembl/", STR(?ensemblId)) AS ?geneIdStr)
+  BIND(URI(?geneIdStr) AS ?geneId)
+  ?gene a orth:Gene .
+  ?gene lscr:xrefEnsemblGene ?geneId .
+  ?expr genex:hasSequenceUnit ?gene.
+  ?expr a genex:Expression .
+  #?expr genex:hasConfidenceLevel obo:CIO_0000029 . # high confidence level
+  ?expr genex:hasConfidenceLevel ?confidenceLevel .
+  ?expr genex:hasExpressionLevel ?expressionLevel .
+  ?expr genex:hasExpressionCondition ?cond .
+  ?cond genex:hasAnatomicalEntity ?anatomicalEntity . # tissue
+  ?anatomicalEntity rdfs:label ?anatomicalEntityName.
+  # also can filter by expression level: e.g. FILTER (?expressionLevel > 99) # highly expressed
+}

src/pyBiodatafuse/annotators/queries/bgee-get-last-modified.rq

@@ -0,0 +1,6 @@
+SELECT DISTINCT (str(?dateModified) as ?dateModified)
+WHERE {
+   <http://purl.org/query/bioquery#BGEE>  <http://purl.org/dc/terms/modified> ?dateModified.
+ }
+ LIMIT 1
+