update experiment evidence codes as per DeepGo SE

- #36 (comment)

Author: aditya0by0

chebai/preprocessing/datasets/go_uniprot.py

@@ -43,6 +43,11 @@
     "IEP",
     "TAS",
     "IC",
+    "HTP",
+    "HDA",
+    "HMP",
+    "HGI",
+    "HEP",
 }
 
 # https://github.com/bio-ontology-research-group/deepgo/blob/d97447a05c108127fee97982fd2c57929b2cf7eb/aaindex.py#L8
@@ -414,7 +419,7 @@ def _get_swiss_to_go_mapping(self) -> pd.DataFrame:
 
             Quote from the DeepGo Paper:
             `We select proteins with annotations having experimental evidence codes
-            (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC) and filter the proteins by a
+            `EXPERIMENTAL_EVIDENCE_CODES` and filter the proteins by a
             maximum length of 1002, ignoring proteins with ambiguous amino acid codes
             (B, O, J, U, X, Z) in their sequence.`
 

chebai/preprocessing/datasets/protein_pretraining.py

@@ -96,8 +96,8 @@ def _download_required_data(self) -> str:
     def _parse_protein_data_for_pretraining(self) -> pd.DataFrame:
         """
         Parses the Swiss-Prot data and returns a DataFrame containing Swiss-Prot proteins which does not have any valid
-        Gene Ontology(GO) label. A valid GO label is the one which has one of the following evidence code
-        (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC).
+        Gene Ontology(GO) label. A valid GO label is the one which has one of the following evidence code defined in
+        `EXPERIMENTAL_EVIDENCE_CODES`.
 
         The DataFrame includes the following columns:
             - "swiss_id": The unique identifier for each Swiss-Prot record.

tests/unit/mock_data/ontology_mock_data.py

@@ -668,8 +668,8 @@ def get_UniProt_raw_data() -> str:
         - **Swiss_Prot_11**: Has only Invalid GO class but lacks a sequence.
 
         Note:
-        A valid GO label is the one which has one of the following evidence code
-        (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC).
+        A valid GO label is the one which has one of the following evidence code defined in
+        `EXPERIMENTAL_EVIDENCE_CODES`.
 
         Returns:
             str: The raw UniProt data in string format.