diff --git a/src/nplinker/__init__.py b/src/nplinker/__init__.py
index 43ace5fe..853775c7 100644
--- a/src/nplinker/__init__.py
+++ b/src/nplinker/__init__.py
@@ -1,5 +1,6 @@
 import logging
-from pathlib import Path
+from .logger import setup_logging
+from .nplinker import NPLinker
 
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())
@@ -9,48 +10,4 @@
 __version__ = "2.0.0-alpha.1"
 
 
-# The path to the NPLinker application database directory
-NPLINKER_APP_DATA_DIR = Path(__file__).parent / "data"
-del Path
-
-
-def setup_logging(level: str = "INFO", file: str = "", use_console: bool = True) -> None:
-    """Setup logging configuration for the ancestor logger "nplinker".
-
-    Args:
-        level: The log level, use the logging module's log level constants. Valid levels are:
-            "NOTSET", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL".
-        file: The file to write the log to. If the file does not exist, it will be created. The log
-            will be written to the file in append mode. If the file is an empty string (by default),
-            the log will not be written to a file.
-        use_console: Whether to log to the console.
-    """
-    from rich.console import Console
-    from rich.logging import RichHandler
-
-    # Get the ancestor logger "nplinker"
-    logger = logging.getLogger(__name__)
-    logger.setLevel(level)
-
-    # File handler
-    if file:
-        logger.addHandler(
-            RichHandler(
-                console=Console(file=open(file, "a"), width=120),  # force the line width to 120
-                omit_repeated_times=False,
-                rich_tracebacks=True,
-                tracebacks_show_locals=True,
-                log_time_format="[%Y-%m-%d %X]",
-            )
-        )
-
-    # Console handler
-    if use_console:
-        logger.addHandler(
-            RichHandler(
-                omit_repeated_times=False,
-                rich_tracebacks=True,
-                tracebacks_show_locals=True,
-                log_time_format="[%Y-%m-%d %X]",
-            )
-        )
+__all__ = ["NPLinker", "setup_logging"]
diff --git a/src/nplinker/arranger.py b/src/nplinker/arranger.py
index 06df9ac5..3a88be7a 100644
--- a/src/nplinker/arranger.py
+++ b/src/nplinker/arranger.py
@@ -1,7 +1,9 @@
+from __future__ import annotations
 import fnmatch
 import json
 import shutil
 from glob import glob
+from os import PathLike
 from pathlib import Path
 from dynaconf import Dynaconf
 from jsonschema import validate
@@ -369,7 +371,7 @@ def arrange_strains_selected(self) -> None:
             validate(instance=json_data, schema=USER_STRAINS_SCHEMA)
 
 
-def validate_gnps(gnps_dir: Path) -> None:
+def validate_gnps(gnps_dir: str | PathLike) -> None:
     """Validate the GNPS data directory and its contents.
 
     The GNPS data directory must contain the following files:
@@ -387,6 +389,7 @@ def validate_gnps(gnps_dir: Path) -> None:
             is not found.
         ValueError: If both file_mappings.tsv and file_mapping.csv are found.
     """
+    gnps_dir = Path(gnps_dir)
     if not gnps_dir.exists():
         raise FileNotFoundError(f"GNPS data directory not found at {gnps_dir}")
 
@@ -415,7 +418,7 @@ def validate_gnps(gnps_dir: Path) -> None:
         )
 
 
-def validate_antismash(antismash_dir: Path) -> None:
+def validate_antismash(antismash_dir: str | PathLike) -> None:
     """Validate the antiSMASH data directory and its contents.
 
     The validation only checks the structure of the antiSMASH data directory and file names.
@@ -438,6 +441,7 @@ def validate_antismash(antismash_dir: Path) -> None:
             sub-directory.
         ValueError: If any sub-directory name contains a space.
     """
+    antismash_dir = Path(antismash_dir)
     if not antismash_dir.exists():
         raise FileNotFoundError(f"antiSMASH data directory not found at {antismash_dir}")
 
@@ -460,7 +464,7 @@ def validate_antismash(antismash_dir: Path) -> None:
             raise FileNotFoundError(f"No BGC files found in antiSMASH sub-directory {sub_dir}")
 
 
-def validate_bigscape(bigscape_dir: Path, cutoff: str) -> None:
+def validate_bigscape(bigscape_dir: str | PathLike, cutoff: str) -> None:
     """Validate the BiG-SCAPE data directory and its contents.
 
     The BiG-SCAPE data directory must exist and contain the clustering file
@@ -478,6 +482,7 @@ def validate_bigscape(bigscape_dir: Path, cutoff: str) -> None:
     Raises:
         FileNotFoundError: If the BiG-SCAPE data directory or the clustering file is not found.
     """
+    bigscape_dir = Path(bigscape_dir)
     if not bigscape_dir.exists():
         raise FileNotFoundError(f"BiG-SCAPE data directory not found at {bigscape_dir}")
 
diff --git a/src/nplinker/defaults.py b/src/nplinker/defaults.py
index a6d53050..65ef08a1 100644
--- a/src/nplinker/defaults.py
+++ b/src/nplinker/defaults.py
@@ -1,18 +1,26 @@
-STRAIN_MAPPINGS_FILENAME = "strain_mappings.json"
-GENOME_BGC_MAPPINGS_FILENAME = "genome_bgc_mappings.json"
-GENOME_STATUS_FILENAME = "genome_status.json"
-GNPS_SPECTRA_FILENAME = "spectra.mgf"
-GNPS_MOLECULAR_FAMILY_FILENAME = "molecular_families.tsv"
-GNPS_ANNOTATIONS_FILENAME = "annotations.tsv"
-GNPS_FILE_MAPPINGS_TSV = "file_mappings.tsv"
-GNPS_FILE_MAPPINGS_CSV = "file_mappings.csv"
-STRAINS_SELECTED_FILENAME = "strains_selected.json"
+from pathlib import Path
+from typing import Final
 
 
-DOWNLOADS_DIRNAME = "downloads"
-MIBIG_DIRNAME = "mibig"
-GNPS_DIRNAME = "gnps"
-ANTISMASH_DIRNAME = "antismash"
-BIGSCAPE_DIRNAME = "bigscape"
-BIGSCAPE_RUNNING_OUTPUT_DIRNAME = "bigscape_running_output"
-OUTPUT_DIRNAME = "output"
+# The path to the NPLinker application database directory
+NPLINKER_APP_DATA_DIR: Final = Path(__file__).parent / "data"
+
+
+STRAIN_MAPPINGS_FILENAME: Final = "strain_mappings.json"
+GENOME_BGC_MAPPINGS_FILENAME: Final = "genome_bgc_mappings.json"
+GENOME_STATUS_FILENAME: Final = "genome_status.json"
+GNPS_SPECTRA_FILENAME: Final = "spectra.mgf"
+GNPS_MOLECULAR_FAMILY_FILENAME: Final = "molecular_families.tsv"
+GNPS_ANNOTATIONS_FILENAME: Final = "annotations.tsv"
+GNPS_FILE_MAPPINGS_TSV: Final = "file_mappings.tsv"
+GNPS_FILE_MAPPINGS_CSV: Final = "file_mappings.csv"
+STRAINS_SELECTED_FILENAME: Final = "strains_selected.json"
+
+
+DOWNLOADS_DIRNAME: Final = "downloads"
+MIBIG_DIRNAME: Final = "mibig"
+GNPS_DIRNAME: Final = "gnps"
+ANTISMASH_DIRNAME: Final = "antismash"
+BIGSCAPE_DIRNAME: Final = "bigscape"
+BIGSCAPE_RUNNING_OUTPUT_DIRNAME: Final = "bigscape_running_output"
+OUTPUT_DIRNAME: Final = "output"
diff --git a/src/nplinker/genomics/abc.py b/src/nplinker/genomics/abc.py
index daeb3bef..53dc0e7e 100644
--- a/src/nplinker/genomics/abc.py
+++ b/src/nplinker/genomics/abc.py
@@ -1,5 +1,7 @@
+from __future__ import annotations
 from abc import ABC
 from abc import abstractmethod
+from os import PathLike
 from .bgc import BGC
 from .gcf import GCF
 
@@ -7,14 +9,14 @@
 class BGCLoaderBase(ABC):
     """Abstract base class for BGC loader."""
 
-    def __init__(self, data_dir: str) -> None:
+    def __init__(self, data_dir: str | PathLike) -> None:
         """Initialize the BGC loader.
 
         Args:
             data_dir: Path to directory that contains BGC metadata files
                 (.json) or full data genbank files (.gbk).
         """
-        self.data_dir = data_dir
+        self.data_dir = str(data_dir)
 
     @abstractmethod
     def get_files(self) -> dict[str, str]:
diff --git a/src/nplinker/genomics/antismash/antismash_loader.py b/src/nplinker/genomics/antismash/antismash_loader.py
index 4c6bd991..0994a212 100644
--- a/src/nplinker/genomics/antismash/antismash_loader.py
+++ b/src/nplinker/genomics/antismash/antismash_loader.py
@@ -2,7 +2,9 @@
 import fnmatch
 import logging
 import os
-from typing import Mapping
+from collections.abc import Mapping
+from os import PathLike
+from pathlib import Path
 from Bio import SeqIO
 from Bio import SeqRecord
 from nplinker.genomics import BGC
@@ -15,7 +17,7 @@
 logger = logging.getLogger(__name__)
 
 
-class AntismashBGCLoader:
+class AntismashBGCLoader(BGCLoaderBase):
     """Build a loader for AntiSMASH BGC genbank (.gbk) files.
 
     Note:
@@ -32,14 +34,14 @@ class AntismashBGCLoader:
         ```
     """
 
-    def __init__(self, data_dir: str) -> None:
+    def __init__(self, data_dir: str | PathLike) -> None:
         """Initialize the AntiSMASH BGC loader.
 
         Args:
             data_dir: Path to AntiSMASH directory that contains a
                 collection of AntiSMASH outputs.
         """
-        self.data_dir = data_dir
+        self.data_dir = str(data_dir)
         self._file_dict = self._parse_data_dir(self.data_dir)
         self._bgcs = self._parse_bgcs(self._file_dict)
 
@@ -111,7 +113,7 @@ def _parse_bgcs(bgc_files: Mapping[str, str]) -> list[BGC]:
         return [parse_bgc_genbank(file) for file in bgc_files.values()]
 
 
-def parse_bgc_genbank(file: str) -> BGC:
+def parse_bgc_genbank(file: str | PathLike) -> BGC:
     """Parse a single BGC gbk file to BGC object.
 
     Args:
@@ -124,7 +126,8 @@ def parse_bgc_genbank(file: str) -> BGC:
         >>> bgc = AntismashBGCLoader.parse_bgc(
         ...    "/data/antismash/GCF_000016425.1/NC_009380.1.region001.gbk")
     """
-    fname = os.path.splitext(os.path.basename(file))[0]
+    file = Path(file)
+    fname = file.stem
 
     record = SeqIO.read(file, format="genbank")
     description = record.description  # "DEFINITION" in gbk file
@@ -138,7 +141,7 @@ def parse_bgc_genbank(file: str) -> BGC:
     bgc = BGC(fname, *product_prediction)
     bgc.description = description
     bgc.antismash_id = antismash_id
-    bgc.antismash_file = file
+    bgc.antismash_file = str(file)
     bgc.antismash_region = features.get("region_number")
     bgc.smiles = features.get("smiles")
     bgc.strain = Strain(fname)
@@ -160,7 +163,3 @@ def _parse_antismash_genbank(record: SeqRecord.SeqRecord) -> dict:
                 smiles = tuple(i.replace(" ", "") for i in smiles)
             features["smiles"] = smiles
     return features
-
-
-# register as virtual class to prevent metaclass conflicts
-BGCLoaderBase.register(AntismashBGCLoader)
diff --git a/src/nplinker/genomics/antismash/podp_antismash_downloader.py b/src/nplinker/genomics/antismash/podp_antismash_downloader.py
index 2a77cc20..1d1bf0b6 100644
--- a/src/nplinker/genomics/antismash/podp_antismash_downloader.py
+++ b/src/nplinker/genomics/antismash/podp_antismash_downloader.py
@@ -3,10 +3,10 @@
 import logging
 import re
 import time
+from collections.abc import Mapping
+from collections.abc import Sequence
 from os import PathLike
 from pathlib import Path
-from typing import Mapping
-from typing import Sequence
 import httpx
 from bs4 import BeautifulSoup
 from bs4 import NavigableString
diff --git a/src/nplinker/genomics/bigscape/bigscape_loader.py b/src/nplinker/genomics/bigscape/bigscape_loader.py
index c4e7637b..f38f47af 100644
--- a/src/nplinker/genomics/bigscape/bigscape_loader.py
+++ b/src/nplinker/genomics/bigscape/bigscape_loader.py
@@ -10,7 +10,7 @@
 logger = logging.getLogger(__name__)
 
 
-class BigscapeGCFLoader:
+class BigscapeGCFLoader(GCFLoaderBase):
     """Build a loader for BiG-SCAPE GCF cluster file.
 
     Attributes:
@@ -61,11 +61,7 @@ def _parse_gcf(cluster_file: str) -> list[GCF]:
         return list(gcf_dict.values())
 
 
-# register as virtual class to prevent metaclass conflicts
-GCFLoaderBase.register(BigscapeGCFLoader)
-
-
-class BigscapeV2GCFLoader:
+class BigscapeV2GCFLoader(GCFLoaderBase):
     """Build a loader for BiG-SCAPE v2 database file.
 
     Attributes:
@@ -137,7 +133,3 @@ def _parse_gcf(db_file: str) -> list[GCF]:
                 gcf_dict[family_id].bgc_ids.add(bgc_id)
 
         return list(gcf_dict.values())
-
-
-# register as virtual class to prevent metaclass conflicts
-GCFLoaderBase.register(BigscapeV2GCFLoader)
diff --git a/src/nplinker/genomics/mibig/mibig_loader.py b/src/nplinker/genomics/mibig/mibig_loader.py
index 3d8eab6b..b588a189 100644
--- a/src/nplinker/genomics/mibig/mibig_loader.py
+++ b/src/nplinker/genomics/mibig/mibig_loader.py
@@ -1,5 +1,7 @@
+from __future__ import annotations
 import logging
-import os.path
+from os import PathLike
+from pathlib import Path
 from nplinker.strain import Strain
 from nplinker.utils import list_files
 from ..abc import BGCLoaderBase
@@ -10,7 +12,7 @@
 logger = logging.getLogger(__name__)
 
 
-class MibigLoader:
+class MibigLoader(BGCLoaderBase):
     """Parse MIBiG metadata files and return BGC objects.
 
     MIBiG metadata file (json) contains annotations/metadata information
@@ -20,13 +22,13 @@ class MibigLoader:
     objects have Strain object as their strain attribute (i.e. `BGC.strain`).
     """
 
-    def __init__(self, data_dir: str):
+    def __init__(self, data_dir: str | PathLike):
         """Initialize the MIBiG metadata loader.
 
         Args:
             data_dir: Path to the directory of MIBiG metadata json files
         """
-        self.data_dir = data_dir
+        self.data_dir = str(data_dir)
         self._file_dict = self.parse_data_dir(self.data_dir)
         self._metadata_dict = self._parse_metadata()
         self._bgcs = self._parse_bgcs()
@@ -41,7 +43,7 @@ def get_files(self) -> dict[str, str]:
         return self._file_dict
 
     @staticmethod
-    def parse_data_dir(data_dir: str) -> dict[str, str]:
+    def parse_data_dir(data_dir: str | PathLike) -> dict[str, str]:
         """Parse metadata directory and return paths to all metadata json files.
 
         Args:
@@ -54,7 +56,7 @@ def parse_data_dir(data_dir: str) -> dict[str, str]:
         file_dict = {}
         json_files = list_files(data_dir, prefix="BGC", suffix=".json")
         for file in json_files:
-            fname = os.path.splitext(os.path.basename(file))[0]
+            fname = Path(file).stem
             file_dict[fname] = file
         return file_dict
 
@@ -99,7 +101,7 @@ def _parse_bgcs(self) -> list[BGC]:
         return [parse_bgc_metadata_json(file) for file in self._file_dict.values()]
 
 
-def parse_bgc_metadata_json(file: str) -> BGC:
+def parse_bgc_metadata_json(file: str | PathLike) -> BGC:
     """Parse MIBiG metadata file and return BGC object.
 
     Note that the MiBIG accession is used as the BGC id and strain name. The BGC
@@ -111,12 +113,8 @@ def parse_bgc_metadata_json(file: str) -> BGC:
     Returns:
         BGC object
     """
-    metadata = MibigMetadata(file)
+    metadata = MibigMetadata(str(file))
     mibig_bgc = BGC(metadata.mibig_accession, *metadata.biosyn_class)
     mibig_bgc.mibig_bgc_class = metadata.biosyn_class
     mibig_bgc.strain = Strain(metadata.mibig_accession)
     return mibig_bgc
-
-
-# register as virtual class to prevent metaclass conflicts
-BGCLoaderBase.register(MibigLoader)
diff --git a/src/nplinker/genomics/mibig/mibig_metadata.py b/src/nplinker/genomics/mibig/mibig_metadata.py
index 4abcbdf8..ebef8685 100644
--- a/src/nplinker/genomics/mibig/mibig_metadata.py
+++ b/src/nplinker/genomics/mibig/mibig_metadata.py
@@ -1,4 +1,6 @@
+from __future__ import annotations
 import json
+from os import PathLike
 
 
 class MibigMetadata:
@@ -9,7 +11,7 @@ class MibigMetadata:
     https://mibig.secondarymetabolites.org/download.
     """
 
-    def __init__(self, file: str) -> None:
+    def __init__(self, file: str | PathLike) -> None:
         """Initialize the MIBiG metadata object.
 
         Args:
@@ -18,7 +20,7 @@ def __init__(self, file: str) -> None:
         Examples:
             >>> metadata = MibigMetadata("/data/BGC0000001.json")
         """
-        self.file = file
+        self.file = str(file)
         with open(self.file, "rb") as f:
             self.metadata = json.load(f)
 
diff --git a/src/nplinker/genomics/utils.py b/src/nplinker/genomics/utils.py
index 41b65316..fd861b9f 100644
--- a/src/nplinker/genomics/utils.py
+++ b/src/nplinker/genomics/utils.py
@@ -1,10 +1,10 @@
 from __future__ import annotations
 import json
 import logging
+from collections.abc import Mapping
+from collections.abc import Sequence
 from os import PathLike
 from pathlib import Path
-from typing import Mapping
-from typing import Sequence
 from jsonschema import validate
 from nplinker.defaults import GENOME_BGC_MAPPINGS_FILENAME
 from nplinker.schemas import GENOME_BGC_MAPPINGS_SCHEMA
diff --git a/src/nplinker/loader.py b/src/nplinker/loader.py
index 3f248bec..db817f79 100644
--- a/src/nplinker/loader.py
+++ b/src/nplinker/loader.py
@@ -3,8 +3,8 @@
 import os
 from deprecated import deprecated
 from dynaconf import Dynaconf
-from nplinker import NPLINKER_APP_DATA_DIR
 from nplinker import defaults
+from nplinker.defaults import NPLINKER_APP_DATA_DIR
 from nplinker.genomics import BGC
 from nplinker.genomics import GCF
 from nplinker.genomics.antismash import AntismashBGCLoader
diff --git a/src/nplinker/logger.py b/src/nplinker/logger.py
new file mode 100644
index 00000000..b02491ee
--- /dev/null
+++ b/src/nplinker/logger.py
@@ -0,0 +1,42 @@
+import logging
+from rich.console import Console
+from rich.logging import RichHandler
+
+
+def setup_logging(level: str = "INFO", file: str = "", use_console: bool = True) -> None:
+    """Setup logging configuration for the ancestor logger "nplinker".
+
+    Args:
+        level: The log level, use the logging module's log level constants. Valid levels are:
+            "NOTSET", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL".
+        file: The file to write the log to. If the file does not exist, it will be created. The log
+            will be written to the file in append mode. If the file is an empty string (by default),
+            the log will not be written to a file.
+        use_console: Whether to log to the console.
+    """
+    # Get the ancestor logger "nplinker"
+    logger = logging.getLogger("nplinker")
+    logger.setLevel(level)
+
+    # File handler
+    if file:
+        logger.addHandler(
+            RichHandler(
+                console=Console(file=open(file, "a"), width=120),  # force the line width to 120
+                omit_repeated_times=False,
+                rich_tracebacks=True,
+                tracebacks_show_locals=True,
+                log_time_format="[%Y-%m-%d %X]",
+            )
+        )
+
+    # Console handler
+    if use_console:
+        logger.addHandler(
+            RichHandler(
+                omit_repeated_times=False,
+                rich_tracebacks=True,
+                tracebacks_show_locals=True,
+                log_time_format="[%Y-%m-%d %X]",
+            )
+        )
diff --git a/src/nplinker/metabolomics/abc.py b/src/nplinker/metabolomics/abc.py
index 6af3052e..dced9252 100644
--- a/src/nplinker/metabolomics/abc.py
+++ b/src/nplinker/metabolomics/abc.py
@@ -1,3 +1,4 @@
+from __future__ import annotations
 from abc import ABC
 from abc import abstractmethod
 from .molecular_family import MolecularFamily
@@ -9,7 +10,7 @@ class SpectrumLoaderBase(ABC):
 
     @property
     @abstractmethod
-    def spectra(self) -> list["Spectrum"]:
+    def spectra(self) -> list[Spectrum]:
         """Get Spectrum objects.
 
         Returns:
@@ -21,7 +22,7 @@ class MolecularFamilyLoaderBase(ABC):
     """Abstract base class for MolecularFamilyLoader."""
 
     @abstractmethod
-    def get_mfs(self, keep_singleton: bool) -> list["MolecularFamily"]:
+    def get_mfs(self, keep_singleton: bool) -> list[MolecularFamily]:
         """Get MolecularFamily objects.
 
         Args:
diff --git a/src/nplinker/metabolomics/utils.py b/src/nplinker/metabolomics/utils.py
index 1110fb7d..0f55ef12 100644
--- a/src/nplinker/metabolomics/utils.py
+++ b/src/nplinker/metabolomics/utils.py
@@ -1,10 +1,10 @@
 from __future__ import annotations
 import json
 import logging
+from collections.abc import Mapping
+from collections.abc import Sequence
 from os import PathLike
 from pathlib import Path
-from typing import Mapping
-from typing import Sequence
 from nplinker.schemas import validate_podp_json
 from nplinker.strain import StrainCollection
 from .gnps.gnps_file_mapping_loader import GNPSFileMappingLoader
diff --git a/src/nplinker/nplinker.py b/src/nplinker/nplinker.py
index e0455b62..80752633 100644
--- a/src/nplinker/nplinker.py
+++ b/src/nplinker/nplinker.py
@@ -1,18 +1,18 @@
 from __future__ import annotations
 import logging
 import pickle
+from collections.abc import Sequence
 from os import PathLike
 from pprint import pformat
-from typing import Sequence
-from typing import TypeVar
+from typing import Any
 from typing import overload
-from . import setup_logging
 from .arranger import DatasetArranger
 from .config import load_config
 from .defaults import OUTPUT_DIRNAME
 from .genomics import BGC
 from .genomics import GCF
 from .loader import DatasetLoader
+from .logger import setup_logging
 from .metabolomics import MolecularFamily
 from .metabolomics import Spectrum
 from .scoring.link_graph import LinkGraph
@@ -22,8 +22,6 @@
 
 logger = logging.getLogger(__name__)
 
-ObjectType = TypeVar("ObjectType", BGC, GCF, Spectrum, MolecularFamily)
-
 
 class NPLinker:
     """Main class for the NPLinker application.
@@ -191,22 +189,27 @@ def load_data(self):
 
     @overload
     def get_links(
-        self, objects: Sequence[BGC], scoring_method: str, **scoring_params
+        self, objects: Sequence[BGC], scoring_method: str, **scoring_params: Any
     ) -> LinkGraph: ...
     @overload
     def get_links(
-        self, objects: Sequence[GCF], scoring_method: str, **scoring_params
+        self, objects: Sequence[GCF], scoring_method: str, **scoring_params: Any
     ) -> LinkGraph: ...
     @overload
     def get_links(
-        self, objects: Sequence[Spectrum], scoring_method: str, **scoring_params
+        self, objects: Sequence[Spectrum], scoring_method: str, **scoring_params: Any
     ) -> LinkGraph: ...
     @overload
     def get_links(
-        self, objects: Sequence[MolecularFamily], scoring_method: str, **scoring_params
+        self, objects: Sequence[MolecularFamily], scoring_method: str, **scoring_params: Any
     ) -> LinkGraph: ...
 
-    def get_links(self, objects, scoring_method, **scoring_params):
+    def get_links(
+        self,
+        objects: Sequence[BGC] | Sequence[GCF] | Sequence[Spectrum] | Sequence[MolecularFamily],
+        scoring_method: str,
+        **scoring_params: Any,
+    ) -> LinkGraph:
         """Get the links for the given objects using the specified scoring method and parameters.
 
         Args:
@@ -214,7 +217,7 @@ def get_links(self, objects, scoring_method, **scoring_params):
                 type, i.e. `BGC`, `GCF`, `Spectrum` or `MolecularFamily` type.
                 For scoring method `metcalf`, the BGC objects are not supported.
             scoring_method: The scoring method to use. Must be one of the valid scoring methods
-                `self.scoring_methods`.
+                `self.scoring_methods`, such as "metcalf".
             scoring_params: Parameters to pass to the scoring method. If not provided, the default
                 parameters for the scoring method will be used.
 
diff --git a/src/nplinker/scoring/__init__.py b/src/nplinker/scoring/__init__.py
index 597fa4f9..6fcaac9c 100644
--- a/src/nplinker/scoring/__init__.py
+++ b/src/nplinker/scoring/__init__.py
@@ -1,4 +1,3 @@
-from .abc import ScoringBase
 from .link_graph import LinkGraph
 from .metcalf_scoring import MetcalfScoring
 from .score import Score
@@ -9,6 +8,5 @@
     "LinkGraph",
     "MetcalfScoring",
     "Score",
-    "ScoringBase",
     "ScoringMethod",
 ]
diff --git a/src/nplinker/scoring/link_graph.py b/src/nplinker/scoring/link_graph.py
index ce1a06b6..316ec450 100644
--- a/src/nplinker/scoring/link_graph.py
+++ b/src/nplinker/scoring/link_graph.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 from functools import wraps
+from typing import Union
 from networkx import Graph
 from nplinker.genomics import GCF
 from nplinker.metabolomics import MolecularFamily
@@ -8,11 +9,17 @@
 from .scoring_method import ScoringMethod
 
 
+# Type aliases
+Entity = Union[GCF, Spectrum, MolecularFamily]  # using Union to ensure python 3.9 compatibility
+LINK_DATA = dict[str, Score]
+LINK = tuple[Entity, Entity, LINK_DATA]
+
+
 def validate_u(func):
     """A decorator to validate the type of the u object."""
 
     @wraps(func)
-    def wrapper(self, u: GCF | Spectrum | MolecularFamily, *args, **kwargs):
+    def wrapper(self, u: Entity, *args, **kwargs):
         if not isinstance(u, (GCF, Spectrum, MolecularFamily)):
             raise TypeError(f"{u} is not a GCF, Spectrum, or MolecularFamily object.")
 
@@ -27,8 +34,8 @@ def validate_uv(func):
     @wraps(func)
     def wrapper(
         self,
-        u: GCF | Spectrum | MolecularFamily,
-        v: GCF | Spectrum | MolecularFamily,
+        u: Entity,
+        v: Entity,
         *args,
         **kwargs,
     ):
@@ -94,9 +101,7 @@ def __len__(self) -> int:
         return len(self._g)
 
     @validate_u
-    def __getitem__(
-        self, u: GCF | Spectrum | MolecularFamily
-    ) -> dict[GCF | Spectrum | MolecularFamily, dict[str, Score]]:
+    def __getitem__(self, u: Entity) -> dict[Entity, LINK_DATA]:
         """Get all links for a given object.
 
         Args:
@@ -118,9 +123,7 @@ def __getitem__(
     @property
     def links(
         self,
-    ) -> list[
-        tuple[GCF | Spectrum | MolecularFamily, GCF | Spectrum | MolecularFamily, dict[str, Score]]
-    ]:
+    ) -> list[LINK]:
         """Get all links.
 
         Returns:
@@ -131,8 +134,8 @@ def links(
     @validate_uv
     def add_link(
         self,
-        u: GCF | Spectrum | MolecularFamily,
-        v: GCF | Spectrum | MolecularFamily,
+        u: Entity,
+        v: Entity,
         **data: Score,
     ) -> None:
         """Add a link between two objects.
@@ -161,9 +164,7 @@ def add_link(
         self._g.add_edge(u, v, **data)
 
     @validate_uv
-    def has_link(
-        self, u: GCF | Spectrum | MolecularFamily, v: GCF | Spectrum | MolecularFamily
-    ) -> bool:
+    def has_link(self, u: Entity, v: Entity) -> bool:
         """Check if there is a link between two objects.
 
         Args:
@@ -178,9 +179,9 @@ def has_link(
     @validate_uv
     def get_link_data(
         self,
-        u: GCF | Spectrum | MolecularFamily,
-        v: GCF | Spectrum | MolecularFamily,
-    ) -> dict[str, Score] | None:
+        u: Entity,
+        v: Entity,
+    ) -> LINK_DATA | None:
         """Get the data for a link between two objects.
 
         Args:
diff --git a/src/nplinker/scoring/metcalf_scoring.py b/src/nplinker/scoring/metcalf_scoring.py
index bc5f31b9..05a6718b 100644
--- a/src/nplinker/scoring/metcalf_scoring.py
+++ b/src/nplinker/scoring/metcalf_scoring.py
@@ -2,7 +2,8 @@
 import logging
 from enum import Enum
 from typing import TYPE_CHECKING
-from typing import TypeVar
+from typing import Union
+from typing import Any
 from typing import overload
 import numpy as np
 import pandas as pd
@@ -33,7 +34,7 @@ class LinkType(Enum):
     MF_GCF = "mf-gcf"
 
 
-ObjectType = TypeVar("ObjectType", GCF, Spectrum, MolecularFamily)
+Entity = Union[GCF, Spectrum, MolecularFamily]
 
 
 class MetcalfScoring(ScoringBase):
@@ -135,19 +136,19 @@ def setup(cls, npl: NPLinker):
         logger.info("MetcalfScoring.setup completed")
 
     @overload
-    def get_links(self, *objects: GCF, **parameters) -> LinkGraph: ...
+    def get_links(self, *objects: GCF, **parameters: Any) -> LinkGraph: ...
     @overload
-    def get_links(self, *objects: Spectrum, **parameters) -> LinkGraph: ...
+    def get_links(self, *objects: Spectrum, **parameters: Any) -> LinkGraph: ...
     @overload
-    def get_links(self, *objects: MolecularFamily, **parameters) -> LinkGraph: ...
+    def get_links(self, *objects: MolecularFamily, **parameters: Any) -> LinkGraph: ...
 
     def get_links(self, *objects, **parameters):
         """Get links for the given objects.
 
         Args:
             objects: The objects to get links for. All objects must be of the same type, i.e. `GCF`,
-              `Spectrum` or `MolecularFamily` type.
-               If no objects are provided, all detected objects (`npl.gcfs`) will be used.
+                `Spectrum` or `MolecularFamily` type.
+                If no objects are provided, all detected objects (`npl.gcfs`) will be used.
             parameters: The scoring parameters to use for the links. The parameters are:
 
                     - cutoff: The minimum score to consider a link (≥cutoff). Default is 0.
@@ -155,7 +156,7 @@ def get_links(self, *objects, **parameters):
 
         Returns:
             The `LinkGraph` object containing the links involving the input objects with the Metcalf
-            scores.
+                scores.
 
         Raises:
             TypeError: If the input objects are not of the same type or the object type is invalid.
@@ -293,8 +294,8 @@ def _calc_mean_std(
 
     def _get_links(
         self,
-        *objects: ObjectType,
-        obj_type: GCF | Spectrum | MolecularFamily,
+        *objects: Entity,
+        obj_type: Entity,
         score_cutoff: float = 0,
     ) -> list[pd.DataFrame]:
         """Get links and scores for the given objects.
diff --git a/src/nplinker/scoring/rosetta/rosetta.py b/src/nplinker/scoring/rosetta/rosetta.py
index 524b7a42..91dfde10 100644
--- a/src/nplinker/scoring/rosetta/rosetta.py
+++ b/src/nplinker/scoring/rosetta/rosetta.py
@@ -14,6 +14,7 @@
 import csv
 import logging
 import os
+from nplinker.defaults import NPLINKER_APP_DATA_DIR
 from nplinker.scoring.rosetta.rosetta_hit import RosettaHit
 from ...genomics import BGC
 from ...parsers.kcb import KCBJSONParser
@@ -21,7 +22,6 @@
 from ...pickler import load_pickled_data
 from ...pickler import save_pickled_data
 from .spec_lib import SpecLib
-from nplinker import NPLINKER_APP_DATA_DIR
 
 
 logger = logging.getLogger(__name__)
diff --git a/src/nplinker/scoring/utils.py b/src/nplinker/scoring/utils.py
index 35b2fbff..0b0cc9de 100644
--- a/src/nplinker/scoring/utils.py
+++ b/src/nplinker/scoring/utils.py
@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import Sequence
+from collections.abc import Sequence
 import pandas as pd
 from nplinker.genomics import GCF
 from nplinker.metabolomics import MolecularFamily
diff --git a/src/nplinker/strain/strain_collection.py b/src/nplinker/strain/strain_collection.py
index 26cd8852..50ca1a3f 100644
--- a/src/nplinker/strain/strain_collection.py
+++ b/src/nplinker/strain/strain_collection.py
@@ -1,8 +1,8 @@
 from __future__ import annotations
 import json
 import logging
+from collections.abc import Iterator
 from os import PathLike
-from typing import Iterator
 from jsonschema import validate
 from nplinker.schemas import STRAIN_MAPPINGS_SCHEMA
 from .strain import Strain
diff --git a/src/nplinker/utils.py b/src/nplinker/utils.py
index c28d14fd..a2777355 100644
--- a/src/nplinker/utils.py
+++ b/src/nplinker/utils.py
@@ -24,10 +24,11 @@
 import sys
 import tarfile
 import zipfile
+from collections.abc import Callable
+from collections.abc import Sequence
 from os import PathLike
 from pathlib import Path
 from typing import IO
-from typing import Callable, Sequence
 import httpx
 from rich.progress import BarColumn
 from rich.progress import DownloadColumn
diff --git a/tests/unit/genomics/test_mibig_metadata.py b/tests/unit/genomics/test_mibig_metadata.py
index 5474f865..738db8d3 100644
--- a/tests/unit/genomics/test_mibig_metadata.py
+++ b/tests/unit/genomics/test_mibig_metadata.py
@@ -8,7 +8,7 @@ class TestMibigMetadata:
     @pytest.fixture
     def json_file(self, version):
         json_file = DATA_DIR / "mibig" / f"BGC0000001_{version}.json"
-        yield json_file
+        yield str(json_file)
 
     @pytest.fixture
     def metadata(self, json_file):