add example

examples/string-linkml-writer/metadata.yaml

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+ingest_title: 'String DB'
+ingest_url: 'https://string-db.org'
+description: 'STRING: functional protein association networks'
+rights: 'https://string-db.org/cgi/access.pl?footer_active_subpage=licensing'

examples/string-linkml-writer/protein-links-detailed.py

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+import uuid
+
+from biolink_model.datamodel.pydanticmodel_v2 import PairwiseGeneToGeneInteraction, Gene
+
+from koza.cli_utils import get_koza_app
+
+koza_app = get_koza_app('protein-links-detailed')
+koza_map = koza_app.get_map('entrez-2-string')
+
+while (row := koza_app.get_row()) is not None:
+    gene_a = Gene(id="NCBIGene:" + koza_map[row["protein1"]]["entrez"])
+    gene_b = Gene(id="NCBIGene:" + koza_map[row["protein2"]]["entrez"])
+
+    pairwise_gene_to_gene_interaction = PairwiseGeneToGeneInteraction(
+        id="uuid:" + str(uuid.uuid1()),
+        subject=gene_a.id,
+        object=gene_b.id,
+        predicate="biolink:interacts_with",
+        knowledge_level="not_provided",
+        agent_type="not_provided",
+    )
+    koza_app.write(gene_a, gene_b, writer="nodes")
+    koza_app.write(pairwise_gene_to_gene_interaction, writer="edges")
+    koza_app.write()

examples/string-linkml-writer/protein-links-detailed.yaml

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+name: 'protein-links-detailed'
+
+delimiter: ' '
+
+files:
+  - './examples/data/string.tsv'
+  - './examples/data/string2.tsv'
+
+metadata: !include './examples/string/metadata.yaml'
+
+columns:
+  - 'protein1'
+  - 'protein2'
+  - 'neighborhood'
+  - 'fusion'
+  - 'cooccurence'
+  - 'coexpression'
+  - 'experimental'
+  - 'database'
+  - 'textmining'
+  - 'combined_score' : 'int'
+
+filters:
+  - inclusion: 'include'
+    column: 'combined_score'
+    filter_code: 'lt'
+    value: 700
+
+depends_on:
+  - './examples/maps/entrez-2-string.yaml'
+
+writers:
+  "nodes":
+    filename: 'protein_links_nodes.tsv'
+    linkml_schema: 'biolink_model.schema:biolink_model.yaml'
+    classes:
+      - 'Gene'
+  "edges":
+    filename: 'protein_links_edges.tsv'
+    linkml_schema: 'biolink_model.schema:biolink_model.yaml'
+    classes:
+      - 'PairwiseGeneToGeneInteraction'
+
+#node_properties:
+#  - 'id'
+#  - 'category'
+#  - 'provided_by'
+#
+#edge_properties:
+#  - 'id'
+#  - 'subject'
+#  - 'predicate'
+#  - 'object'
+#  - 'category'
+#  - 'relation'
+#  - 'provided_by'
+
+transform_mode: 'loop'