diff --git a/notebooks/npclassscore_linking/prospecting/class_linking.py b/notebooks/npclassscore_linking/prospecting/class_linking.py
index c793be56..355a7be5 100644
--- a/notebooks/npclassscore_linking/prospecting/class_linking.py
+++ b/notebooks/npclassscore_linking/prospecting/class_linking.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Initial code for NPClassScore."""
+
 import glob
 import os
 import sys
@@ -541,7 +542,7 @@ def class_linking_score(self, obj, target):
 
         if is_spectrum:
             # list of list of tuples/None - todo: add to spectrum object
-            spec_like_classes = self.canopus.spectra_classes.get(str(spec_like.spectrum_id))
+            spec_like_classes = self.canopus.spectra_classes.get(str(spec_like.id))
             spec_like_classes_names_inds = self.canopus.spectra_classes_names_inds
         else:  # molfam
             spec_like_classes = self.canopus.molfam_classes.get(str(spec_like.family_id))
@@ -654,7 +655,7 @@ def npclass_score(self, obj, target, method="main"):
             if is_spectrum:
                 # list of list of tuples/None - todo: add to spectrum object
                 # take only 'best' (first) classification per ontology level
-                all_classes = self.canopus.spectra_classes.get(str(spec_like.spectrum_id))
+                all_classes = self.canopus.spectra_classes.get(str(spec_like.id))
                 if all_classes:
                     spec_like_classes = [
                         cls_per_lvl
@@ -675,7 +676,7 @@ def npclass_score(self, obj, target, method="main"):
                 spec_like_classes_names_inds = self.canopus.molfam_classes_names_inds
         if use_mne and not spec_like_classes:  # if mne or when main/canopus does not get classes
             if is_spectrum:
-                spec_like_classes = self.molnetenhancer.spectra_classes(spec_like.spectrum_id)
+                spec_like_classes = self.molnetenhancer.spectra_classes(spec_like.id)
             else:  # molfam
                 spec_like_classes = self.molnetenhancer.molfam_classes.get(str(spec_like.family_id))
             # classes are same for molfam and spectrum so names are irrespective of is_spectrum
@@ -777,4 +778,4 @@ def _get_bgc_like_classes(self, bgc_like, is_bgc):
         return bgc_like_classes_dict
 
     def _get_bgc_like_gcf(self, bgc_like):
-        return [gcf for gcf in self.gcfs if bgc_like.bgc_id in [b.bgc_id for b in gcf.bgcs]][0]
+        return [gcf for gcf in self.gcfs if bgc_like.bgc_id in [b.id for b in gcf.bgcs]][0]
diff --git a/notebooks/npclassscore_linking/prospecting/class_linking_test.py b/notebooks/npclassscore_linking/prospecting/class_linking_test.py
index 6b7af47a..fec525a7 100644
--- a/notebooks/npclassscore_linking/prospecting/class_linking_test.py
+++ b/notebooks/npclassscore_linking/prospecting/class_linking_test.py
@@ -35,8 +35,8 @@
     # 2. check chemical compound predictions from canopus and molnetenhancer
     test_spec = list(npl.spectra)[500]
 
-    print(npl.canopus.spectra_classes.get(str(test_spec.spectrum_id)))
-    print(npl.molnetenhancer.spectra_classes(str(test_spec.spectrum_id)))
+    print(npl.canopus.spectra_classes.get(str(test_spec.id)))
+    print(npl.molnetenhancer.spectra_classes(str(test_spec.id)))
 
     # 3. example of a good score, (predicted) NRP linking to a (predicted) peptide like spectrum
     print(npl.class_linking_score(list(npl.gcfs)[0], test_spec))
diff --git a/src/nplinker/class_info/chem_classes.py b/src/nplinker/class_info/chem_classes.py
index b99f9f47..5bf1327d 100644
--- a/src/nplinker/class_info/chem_classes.py
+++ b/src/nplinker/class_info/chem_classes.py
@@ -396,17 +396,17 @@ class prediction for a level. When no class is present, instead of Tuple it will
         molfam_classes = {}
 
         for molfam in molfams:
-            fid = molfam.family_id  # the key
+            fid = molfam.id  # the key
             spectra = molfam.spectra
             # if singleton family, format like 'fid_spectrum-id'
             if fid.startswith("singleton-"):
-                spec_id = spectra[0].spectrum_id
+                spec_id = spectra[0].id
                 fid += f"_{spec_id}"
             len_molfam = len(spectra)
 
             classes_per_spectra = []
             for spec in spectra:
-                spec_classes = self.spectra_classes.get(spec.spectrum_id)
+                spec_classes = self.spectra_classes.get(spec.id)
                 if spec_classes:  # account for spectra without prediction
                     classes_per_spectra.append(spec_classes)
 
diff --git a/src/nplinker/genomics/bgc.py b/src/nplinker/genomics/bgc.py
index c63c94cb..e291cac0 100644
--- a/src/nplinker/genomics/bgc.py
+++ b/src/nplinker/genomics/bgc.py
@@ -28,7 +28,7 @@ class BGC:
     and used by MIBiG.
 
     Attributes:
-        bgc_id: BGC identifier, e.g. MIBiG accession, GenBank accession.
+        id: BGC identifier, e.g. MIBiG accession, GenBank accession.
         product_prediction: A tuple of (predicted) natural
             products or product classes of the BGC.
             For antiSMASH's GenBank data, the feature `region /product`
@@ -59,15 +59,15 @@ class BGC:
         strain: The strain of the BGC.
     """
 
-    def __init__(self, bgc_id: str, /, *product_prediction: str):
+    def __init__(self, id: str, /, *product_prediction: str):
         """Initialize the BGC object.
 
         Args:
-            bgc_id: BGC identifier, e.g. MIBiG accession, GenBank accession.
+            id: BGC identifier, e.g. MIBiG accession, GenBank accession.
             product_prediction: BGC's (predicted) natural products or product classes.
         """
         # BGC metadata
-        self.bgc_id = bgc_id
+        self.id = id
         self.product_prediction = product_prediction
 
         self.mibig_bgc_class: tuple[str] | None = None
@@ -87,9 +87,9 @@ def __repr__(self):
         return str(self)
 
     def __str__(self):
-        return "{}(bgc_id={}, strain={}, asid={}, region={})".format(
+        return "{}(id={}, strain={}, asid={}, region={})".format(
             self.__class__.__name__,
-            self.bgc_id,
+            self.id,
             self.strain,
             self.antismash_id,
             self.antismash_region,
@@ -97,13 +97,11 @@ def __str__(self):
 
     def __eq__(self, other) -> bool:
         if isinstance(other, BGC):
-            return (
-                self.bgc_id == other.bgc_id and self.product_prediction == other.product_prediction
-            )
+            return self.id == other.id and self.product_prediction == other.product_prediction
         return NotImplemented
 
     def __hash__(self) -> int:
-        return hash((self.bgc_id, self.product_prediction))
+        return hash((self.id, self.product_prediction))
 
     def add_parent(self, gcf: GCF) -> None:
         """Add a parent GCF to the BGC.
@@ -146,7 +144,7 @@ def is_mibig(self) -> bool:
         Returns:
             True if it's MIBiG reference BGC
         """
-        return self.bgc_id.startswith("BGC")
+        return self.id.startswith("BGC")
 
     # CG: why not providing whole product but only amino acid as product monomer?
     # this property is not used in NPLinker core business.
diff --git a/src/nplinker/genomics/gcf.py b/src/nplinker/genomics/gcf.py
index eb5963c0..ecddd7a7 100644
--- a/src/nplinker/genomics/gcf.py
+++ b/src/nplinker/genomics/gcf.py
@@ -18,7 +18,7 @@ class GCF:
     tools such as BiG-SCAPE and BiG-SLICE.
 
     Attributes:
-        gcf_id: id of the GCF object.
+        id: id of the GCF object.
         bgc_ids: a set of BGC ids that belongs to the GCF.
         bigscape_class: BiG-SCAPE's BGC class.
             BiG-SCAPE's BGC classes are similar to those defined in MiBIG
@@ -26,13 +26,13 @@ class GCF:
             https://doi.org/10.1038%2Fs41589-019-0400-9.
     """
 
-    def __init__(self, gcf_id: str, /) -> None:
+    def __init__(self, id: str, /) -> None:
         """Initialize the GCF object.
 
         Args:
-            gcf_id: id of the GCF object.
+            id: id of the GCF object.
         """
-        self.gcf_id = gcf_id
+        self.id = id
         self.bgc_ids: set[str] = set()
         self.bigscape_class: str | None = None
         self._bgcs: set[BGC] = set()
@@ -40,7 +40,7 @@ def __init__(self, gcf_id: str, /) -> None:
 
     def __str__(self) -> str:
         return (
-            f"GCF(id={self.gcf_id}, #BGC_objects={len(self.bgcs)}, #bgc_ids={len(self.bgc_ids)},"
+            f"GCF(id={self.id}, #BGC_objects={len(self.bgcs)}, #bgc_ids={len(self.bgc_ids)},"
             f"#strains={len(self._strains)})."
         )
 
@@ -49,7 +49,7 @@ def __repr__(self) -> str:
 
     def __eq__(self, other) -> bool:
         if isinstance(other, GCF):
-            return self.gcf_id == other.gcf_id and self.bgcs == other.bgcs
+            return self.id == other.id and self.bgcs == other.bgcs
         return NotImplemented
 
     def __hash__(self) -> int:
@@ -58,7 +58,7 @@ def __hash__(self) -> int:
         Note that GCF class is a mutable container. We only hash the GCF id to
         avoid the hash value changes when `self._bgcs` is updated.
         """
-        return hash(self.gcf_id)
+        return hash(self.id)
 
     @property
     def bgcs(self) -> set[BGC]:
@@ -74,17 +74,17 @@ def add_bgc(self, bgc: BGC) -> None:
         """Add a BGC object to the GCF."""
         bgc.parents.add(self)
         self._bgcs.add(bgc)
-        self.bgc_ids.add(bgc.bgc_id)
+        self.bgc_ids.add(bgc.id)
         if bgc.strain is not None:
             self._strains.add(bgc.strain)
         else:
-            logger.warning("No strain specified for the BGC %s", bgc.bgc_id)
+            logger.warning("No strain specified for the BGC %s", bgc.id)
 
     def detach_bgc(self, bgc: BGC) -> None:
         """Remove a child BGC object."""
         bgc.parents.remove(self)
         self._bgcs.remove(bgc)
-        self.bgc_ids.remove(bgc.bgc_id)
+        self.bgc_ids.remove(bgc.id)
         if bgc.strain is not None:
             for other_bgc in self._bgcs:
                 if other_bgc.strain == bgc.strain:
diff --git a/src/nplinker/genomics/utils.py b/src/nplinker/genomics/utils.py
index aa984e20..ba4c227b 100644
--- a/src/nplinker/genomics/utils.py
+++ b/src/nplinker/genomics/utils.py
@@ -91,13 +91,13 @@ def add_strain_to_bgc(strains: StrainCollection, bgcs: list[BGC]) -> tuple[list[
     bgc_without_strain = []
     for bgc in bgcs:
         try:
-            strain_list = strains.lookup(bgc.bgc_id)
+            strain_list = strains.lookup(bgc.id)
         except ValueError:
             bgc_without_strain.append(bgc)
             continue
         if len(strain_list) > 1:
             raise ValueError(
-                f"Multiple strain objects found for BGC id '{bgc.bgc_id}'."
+                f"Multiple strain objects found for BGC id '{bgc.id}'."
                 f"BGC object accept only one strain."
             )
         bgc.strain = strain_list[0]
@@ -136,7 +136,7 @@ def add_bgc_to_gcf(
             - The dictionary contains GCF objects as keys and a set of ids of missing
                 BGC objects as values.
     """
-    bgc_dict = {bgc.bgc_id: bgc for bgc in bgcs}
+    bgc_dict = {bgc.id: bgc for bgc in bgcs}
     gcf_with_bgc = []
     gcf_without_bgc = []
     gcf_missing_bgc: dict[GCF, set[str]] = {}
diff --git a/src/nplinker/metabolomics/gnps/gnps_molecular_family_loader.py b/src/nplinker/metabolomics/gnps/gnps_molecular_family_loader.py
index ac048b03..93589643 100644
--- a/src/nplinker/metabolomics/gnps/gnps_molecular_family_loader.py
+++ b/src/nplinker/metabolomics/gnps/gnps_molecular_family_loader.py
@@ -98,15 +98,15 @@ def _load(self) -> None:
             for row in reader:
                 spec1_id = row["CLUSTERID1"]
                 spec2_id = row["CLUSTERID2"]
-                family_id = row["ComponentIndex"]
-                if family_id not in family_dict:
-                    family_dict[family_id] = set([spec1_id, spec2_id])
+                mf_id = row["ComponentIndex"]
+                if mf_id not in family_dict:
+                    family_dict[mf_id] = set([spec1_id, spec2_id])
                 else:
-                    family_dict[family_id].add(spec1_id)
-                    family_dict[family_id].add(spec2_id)
+                    family_dict[mf_id].add(spec1_id)
+                    family_dict[mf_id].add(spec2_id)
         # convert dict to list of MolecularFamily objects
-        for family_id, spectra_ids in family_dict.items():
-            if family_id == "-1":  # "-1" is from GNPS, it means the singleton molecular family
+        for mf_id, spectra_ids in family_dict.items():
+            if mf_id == "-1":  # "-1" is from GNPS, it means the singleton molecular family
                 for spectrum_id in spectra_ids:
                     # family id must be unique, so using "singleton-" + spectrum id as family id
                     family = MolecularFamily("singleton-" + str(spectrum_id))
@@ -114,6 +114,6 @@ def _load(self) -> None:
                     self._mfs.append(family)
             else:
                 # for regular molecular families, use the value of "ComponentIndex" as family id
-                family = MolecularFamily(family_id)
+                family = MolecularFamily(mf_id)
                 family.spectra_ids = spectra_ids
                 self._mfs.append(family)
diff --git a/src/nplinker/metabolomics/gnps/gnps_spectrum_loader.py b/src/nplinker/metabolomics/gnps/gnps_spectrum_loader.py
index e4d25939..d9b34156 100644
--- a/src/nplinker/metabolomics/gnps/gnps_spectrum_loader.py
+++ b/src/nplinker/metabolomics/gnps/gnps_spectrum_loader.py
@@ -89,7 +89,7 @@ def _load(self):
             rt = spec["params"].get("rtinseconds", 0)
 
             spectrum = Spectrum(
-                spectrum_id=spectrum_id,
+                id=spectrum_id,
                 mz=list(spec["m/z array"]),
                 intensity=list(spec["intensity array"]),
                 precursor_mz=precursor_mz,
diff --git a/src/nplinker/metabolomics/molecular_family.py b/src/nplinker/metabolomics/molecular_family.py
index aaf64b7f..16d9bd6a 100644
--- a/src/nplinker/metabolomics/molecular_family.py
+++ b/src/nplinker/metabolomics/molecular_family.py
@@ -12,24 +12,24 @@ class MolecularFamily:
     """Class to model molecular family.
 
     Attributes:
-        family_id: Unique id for the molecular family.
+        id: Unique id for the molecular family.
         spectra_ids: Set of spectrum ids in the molecular family.
     """
 
-    def __init__(self, family_id: str):
+    def __init__(self, id: str):
         """Initialize the MolecularFamily.
 
         Args:
-            family_id: Unique id for the molecular family.
+            id: Unique id for the molecular family.
         """
-        self.family_id: str = family_id
+        self.id: str = id
         self.spectra_ids: set[str] = set()
         self._spectra: set[Spectrum] = set()
         self._strains: StrainCollection = StrainCollection()
 
     def __str__(self) -> str:
         return (
-            f"MolecularFamily(family_id={self.family_id}, #Spectrum_objects={len(self._spectra)}, "
+            f"MolecularFamily(id={self.id}, #Spectrum_objects={len(self._spectra)}, "
             f"#spectrum_ids={len(self.spectra_ids)}, #strains={len(self._strains)})"
         )
 
@@ -38,11 +38,11 @@ def __repr__(self) -> str:
 
     def __eq__(self, other) -> bool:
         if isinstance(other, MolecularFamily):
-            return self.family_id == other.family_id
+            return self.id == other.id
         return NotImplemented
 
     def __hash__(self) -> int:
-        return hash(self.family_id)
+        return hash(self.id)
 
     @property
     def spectra(self) -> set[Spectrum]:
@@ -61,7 +61,7 @@ def add_spectrum(self, spectrum: Spectrum) -> None:
             spectrum: `Spectrum` object to add to the molecular family.
         """
         self._spectra.add(spectrum)
-        self.spectra_ids.add(spectrum.spectrum_id)
+        self.spectra_ids.add(spectrum.id)
         self._strains = self._strains + spectrum.strains
         # add the molecular family to the spectrum
         spectrum.family = self
@@ -73,7 +73,7 @@ def detach_spectrum(self, spectrum: Spectrum) -> None:
             spectrum: `Spectrum` object to remove from the molecular family.
         """
         self._spectra.remove(spectrum)
-        self.spectra_ids.remove(spectrum.spectrum_id)
+        self.spectra_ids.remove(spectrum.id)
         self._strains = self._update_strains()
         # remove the molecular family from the spectrum
         spectrum.family = None
diff --git a/src/nplinker/metabolomics/spectrum.py b/src/nplinker/metabolomics/spectrum.py
index 53c82b72..5ec7ccb2 100644
--- a/src/nplinker/metabolomics/spectrum.py
+++ b/src/nplinker/metabolomics/spectrum.py
@@ -14,7 +14,7 @@ class Spectrum:
     """Class to model MS/MS Spectrum.
 
     Attributes:
-        spectrum_id: the spectrum ID.
+        id: the spectrum ID.
         mz: the list of m/z values.
         intensity: the list of intensity values.
         precursor_mz: the m/z value of the precursor.
@@ -30,7 +30,7 @@ class Spectrum:
 
     def __init__(
         self,
-        spectrum_id: str,
+        id: str,
         mz: list[float],
         intensity: list[float],
         precursor_mz: float,
@@ -40,7 +40,7 @@ def __init__(
         """Initialize the Spectrum.
 
         Args:
-            spectrum_id: the spectrum ID.
+            id: the spectrum ID.
             mz: the list of m/z values.
             intensity: the list of intensity values.
             precursor_mz: the precursor m/z.
@@ -48,7 +48,7 @@ def __init__(
             metadata: the metadata of the spectrum, i.e. the header infomation
                 in the MGF file.
         """
-        self.spectrum_id = spectrum_id
+        self.id = id
         self.mz = mz
         self.intensity = intensity
         self.precursor_mz = precursor_mz
@@ -61,18 +61,18 @@ def __init__(
         self.family: MolecularFamily | None = None
 
     def __str__(self) -> str:
-        return f"Spectrum(spectrum_id={self.spectrum_id}, #strains={len(self.strains)})"
+        return f"Spectrum(id={self.id}, #strains={len(self.strains)})"
 
     def __repr__(self) -> str:
         return str(self)
 
     def __eq__(self, other) -> bool:
         if isinstance(other, Spectrum):
-            return self.spectrum_id == other.spectrum_id and self.precursor_mz == other.precursor_mz
+            return self.id == other.id and self.precursor_mz == other.precursor_mz
         return NotImplemented
 
     def __hash__(self) -> int:
-        return hash((self.spectrum_id, self.precursor_mz))
+        return hash((self.id, self.precursor_mz))
 
     @cached_property
     def peaks(self) -> np.ndarray:
diff --git a/src/nplinker/metabolomics/utils.py b/src/nplinker/metabolomics/utils.py
index 1f1ce8a0..a8a53aef 100644
--- a/src/nplinker/metabolomics/utils.py
+++ b/src/nplinker/metabolomics/utils.py
@@ -25,8 +25,8 @@ def add_annotation_to_spectrum(annotations: dict[str, dict], spectra: list[Spect
         spectra: A list of Spectrum objects.
     """
     for spec in spectra:
-        if spec.spectrum_id in annotations:
-            spec.gnps_annotations = annotations[spec.spectrum_id]
+        if spec.id in annotations:
+            spec.gnps_annotations = annotations[spec.id]
 
 
 def add_strains_to_spectrum(
@@ -51,7 +51,7 @@ def add_strains_to_spectrum(
     spectra_without_strains = []
     for spec in spectra:
         try:
-            strain_list = strains.lookup(spec.spectrum_id)
+            strain_list = strains.lookup(spec.id)
         except ValueError:
             spectra_without_strains.append(spec)
             continue
@@ -94,7 +94,7 @@ def add_spectrum_to_mf(
             - the third is a dictionary containing MolecularFamily objects as keys and a set of ids
             of missing Spectrum objects as values.
     """
-    spec_dict = {spec.spectrum_id: spec for spec in spectra}
+    spec_dict = {spec.id: spec for spec in spectra}
     mf_with_spec = []
     mf_without_spec = []
     mf_missing_spec: dict[MolecularFamily, set[str]] = {}
diff --git a/src/nplinker/nplinker.py b/src/nplinker/nplinker.py
index dd3f8984..0dff285e 100644
--- a/src/nplinker/nplinker.py
+++ b/src/nplinker/nplinker.py
@@ -262,25 +262,25 @@ def get_links(
         logger.info("Final size of link collection is {}".format(len(link_collection)))
         return link_collection
 
-    def has_bgc(self, bgc_id):
-        """Returns True if BGC ``bgc_id`` exists in the dataset."""
-        return bgc_id in self._bgc_lookup
+    def has_bgc(self, id):
+        """Returns True if BGC ``id`` exists in the dataset."""
+        return id in self._bgc_lookup
 
-    def lookup_bgc(self, bgc_id):
-        """If BGC ``bgc_id`` exists, return it. Otherwise return None."""
-        return self._bgc_lookup.get(bgc_id, None)
+    def lookup_bgc(self, id):
+        """If BGC ``id`` exists, return it. Otherwise return None."""
+        return self._bgc_lookup.get(id, None)
 
-    def lookup_gcf(self, gcf_id):
-        """If GCF ``gcf_id`` exists, return it. Otherwise return None."""
-        return self._gcf_lookup.get(gcf_id, None)
+    def lookup_gcf(self, id):
+        """If GCF ``id`` exists, return it. Otherwise return None."""
+        return self._gcf_lookup.get(id, None)
 
-    def lookup_spectrum(self, spectrum_id):
+    def lookup_spectrum(self, id):
         """If Spectrum ``name`` exists, return it. Otherwise return None."""
-        return self._spec_lookup.get(spectrum_id, None)
+        return self._spec_lookup.get(id, None)
 
-    def lookup_mf(self, mf_id):
-        """If MolecularFamily `family_id` exists, return it. Otherwise return None."""
-        return self._mf_lookup.get(mf_id, None)
+    def lookup_mf(self, id):
+        """If MolecularFamily `id` exists, return it. Otherwise return None."""
+        return self._mf_lookup.get(id, None)
 
     @property
     def strains(self):
diff --git a/src/nplinker/pickler.py b/src/nplinker/pickler.py
index 133ab1fd..c80866a5 100644
--- a/src/nplinker/pickler.py
+++ b/src/nplinker/pickler.py
@@ -39,13 +39,13 @@
 class NPLinkerPickler(pickle.Pickler):
     def persistent_id(self, obj):
         if isinstance(obj, BGC):
-            return ("BGC", obj.bgc_id)
+            return ("BGC", obj.id)
         elif isinstance(obj, GCF):
-            return ("GCF", obj.gcf_id)
+            return ("GCF", obj.id)
         elif isinstance(obj, Spectrum):
-            return ("Spectrum", obj.spectrum_id)
+            return ("Spectrum", obj.id)
         elif isinstance(obj, MolecularFamily):
-            return ("MolecularFamily", obj.family_id)
+            return ("MolecularFamily", obj.id)
         else:
             # TODO: ideally should use isinstance(obj, ScoringMethod) here
             # but it's currently a problem because it creates a circular
diff --git a/src/nplinker/scoring/iokr/nplinker_iokr.py b/src/nplinker/scoring/iokr/nplinker_iokr.py
index 405e19a0..07219e0c 100644
--- a/src/nplinker/scoring/iokr/nplinker_iokr.py
+++ b/src/nplinker/scoring/iokr/nplinker_iokr.py
@@ -136,7 +136,7 @@ def score_smiles(self, ms_list, candidate_smiles):
         candidates = iokr_opt.preprocess_candidates(candidate_fps, latent, latent_basis, gamma)
 
         for ms_index, ms in enumerate(ms_list):
-            logger.debug("Rank spectrum {} ({}/{})".format(ms.spectrum_id, ms_index, len(ms_list)))
+            logger.debug("Rank spectrum {} ({}/{})".format(ms.id, ms_index, len(ms_list)))
             ms.filter = spectrum_filters.filter_by_frozen_dag
             logger.debug("kernel vector")
             t0 = time.time()
diff --git a/src/nplinker/scoring/metcalf_scoring.py b/src/nplinker/scoring/metcalf_scoring.py
index 54b81c18..e868e1f7 100644
--- a/src/nplinker/scoring/metcalf_scoring.py
+++ b/src/nplinker/scoring/metcalf_scoring.py
@@ -387,9 +387,7 @@ def _get_links(
 
         links = []
         if obj_type == "gcf":
-            # TODO CG: the hint and mypy warnings will be gone after renaming all
-            # string ids to `.id`
-            obj_ids = [gcf.gcf_id for gcf in objects]
+            obj_ids = [gcf.id for gcf in objects]
             # spec-gcf
             scores = self.raw_score_spec_gcf.loc[:, obj_ids]
             df = self._get_scores_source_gcf(scores, score_cutoff)
@@ -402,14 +400,14 @@ def _get_links(
             links.append(df)
 
         if obj_type == "spec":
-            obj_ids = [spec.spectrum_id for spec in objects]
+            obj_ids = [spec.id for spec in objects]
             scores = self.raw_score_spec_gcf.loc[obj_ids, :]
             df = self._get_scores_source_met(scores, score_cutoff)
             df.name = LINK_TYPES[0]
             links.append(df)
 
         if obj_type == "mf":
-            obj_ids = [mf.family_id for mf in objects]
+            obj_ids = [mf.id for mf in objects]
             scores = self.raw_score_mf_gcf.loc[obj_ids, :]
             df = self._get_scores_source_met(scores, score_cutoff)
             df.name = LINK_TYPES[1]
diff --git a/src/nplinker/scoring/np_class_scoring.py b/src/nplinker/scoring/np_class_scoring.py
index e351f872..25479512 100644
--- a/src/nplinker/scoring/np_class_scoring.py
+++ b/src/nplinker/scoring/np_class_scoring.py
@@ -213,7 +213,7 @@ def _get_gen_classes(self, bgc_like, gcf_as_cutoff=0.5):
         if is_bgc:
             # get parent gcf for bgc
             bgc_like_gcf = [
-                gcf for gcf in self.npl.gcfs if bgc_like.bgc_id in [b.bgc_id for b in gcf.bgcs]
+                gcf for gcf in self.npl.gcfs if bgc_like.id in [b.id for b in gcf.bgcs]
             ][0]
             # gather AS classes and convert to names in scoring dict
             as_classes = self.npl.class_matches.convert_as_classes(
@@ -269,9 +269,7 @@ def _get_met_classes(self, spec_like, method="mix"):
             if is_spectrum:
                 # list of list of tuples/None - todo: add to spectrum object?
                 # take only 'best' (first) classification per ontology level
-                all_classes = self.npl.chem_classes.canopus.spectra_classes.get(
-                    spec_like.spectrum_id
-                )
+                all_classes = self.npl.chem_classes.canopus.spectra_classes.get(spec_like.id)
                 if all_classes:
                     spec_like_classes = [
                         cls_per_lvl
@@ -283,9 +281,9 @@ def _get_met_classes(self, spec_like, method="mix"):
                     self.npl.chem_classes.canopus.spectra_classes_names_inds
                 )
             else:  # molfam
-                fam_id = spec_like.family_id
+                fam_id = spec_like.family.id
                 if fam_id.startswith("singleton-"):  # account for singleton families
-                    fam_id += f"_{spec_like.spectra[0].spectrum_id}"
+                    fam_id += f"_{spec_like.spectra[0].id}"
                 all_classes = self.npl.chem_classes.canopus.molfam_classes.get(fam_id)
                 if all_classes:
                     spec_like_classes = [
@@ -301,12 +299,12 @@ def _get_met_classes(self, spec_like, method="mix"):
             # if mne or when main/canopus does not get classes
             if is_spectrum:
                 spec_like_classes = self.npl.chem_classes.molnetenhancer.spectra_classes(
-                    spec_like.spectrum_id
+                    spec_like.id
                 )
             else:  # molfam
-                fam_id = spec_like.family_id
+                fam_id = spec_like.family.id
                 if fam_id.startswith("singleton"):  # account for singleton families
-                    fam_id += f"_{spec_like.spectra[0].spectrum_id}"
+                    fam_id += f"_{spec_like.spectra[0].id}"
                 spec_like_classes = self.npl.chem_classes.molnetenhancer.molfam_classes.get(fam_id)
             # classes are same for molfam and spectrum so names are irrespective of is_spectrum
             spec_like_classes_names_inds = (
diff --git a/src/nplinker/scoring/rosetta/rosetta.py b/src/nplinker/scoring/rosetta/rosetta.py
index 3ab7a287..c24f962a 100644
--- a/src/nplinker/scoring/rosetta/rosetta.py
+++ b/src/nplinker/scoring/rosetta/rosetta.py
@@ -547,10 +547,10 @@ def export_to_csv(self, filename):
             for hit in self._rosetta_hits:
                 csvwriter.writerow(
                     [
-                        hit.spec.spectrum_id,
+                        hit.spec.id,
                         hit.gnps_id,
                         hit.spec_match_score,
-                        hit.bgc.bgc_id,
+                        hit.bgc.id,
                         hit.mibig_id,
                         hit.bgc_match_score,
                     ]
diff --git a/src/nplinker/scoring/rosetta/rosetta_hit.py b/src/nplinker/scoring/rosetta/rosetta_hit.py
index dda4a1ef..2ca23872 100644
--- a/src/nplinker/scoring/rosetta/rosetta_hit.py
+++ b/src/nplinker/scoring/rosetta/rosetta_hit.py
@@ -9,8 +9,8 @@ def __init__(self, spec, gnps_id, mibig_id, bgc, spec_match_score, bgc_match_sco
 
     def __str__(self):
         return "RosettaHit: {}<-->{} via ({} ({:.3f}), {} ({:.3f}))".format(
-            self.spec.spectrum_id,
-            self.bgc.bgc_id,
+            self.spec.id,
+            self.bgc.id,
             self.gnps_id,
             self.spec_match_score,
             self.mibig_id,
diff --git a/src/nplinker/scoring/rosetta/spec_lib.py b/src/nplinker/scoring/rosetta/spec_lib.py
index 6896a3a4..d99a413d 100644
--- a/src/nplinker/scoring/rosetta/spec_lib.py
+++ b/src/nplinker/scoring/rosetta/spec_lib.py
@@ -39,7 +39,7 @@ def get_n_spec(self):
         return len(self.spectra)
 
     def get_ids(self):
-        return list(s.spectrum_id for s in self.spectra)
+        return list(s.id for s in self.spectra)
 
     def get_n_peaks(self):
         return [len(s.peaks) for s in self.spectra]
diff --git a/src/nplinker/scoring/rosetta_scoring.py b/src/nplinker/scoring/rosetta_scoring.py
index c8a6ce62..057d14d7 100644
--- a/src/nplinker/scoring/rosetta_scoring.py
+++ b/src/nplinker/scoring/rosetta_scoring.py
@@ -126,7 +126,7 @@ def get_links(self, *objects, **parameters):
     def _collect_results_spectra(self, objects, ro_hits, results):
         for spec in objects:
             for hit in ro_hits:
-                if spec.spectrum_id == hit.spec.spectrum_id:
+                if spec.id == hit.spec.id:
                     if not self.bgc_to_gcf:
                         # can use the BGC directly
                         results = self._insert_result_met(results, spec, hit.bgc, hit)
@@ -141,7 +141,7 @@ def _collect_results_spectra(self, objects, ro_hits, results):
     def _collect_results_bgc(self, objects, ro_hits, results):
         for bgc in objects:
             for hit in ro_hits:
-                if bgc.bgc_id == hit.bgc.bgc_id:
+                if bgc.id == hit.bgc.id:
                     if not self.bgc_to_gcf:
                         # can use the BGC directly
                         results = self._insert_result_gen(results, bgc, hit)
diff --git a/src/nplinker/scoring/utils.py b/src/nplinker/scoring/utils.py
index b3914ae7..a93ed24f 100644
--- a/src/nplinker/scoring/utils.py
+++ b/src/nplinker/scoring/utils.py
@@ -21,19 +21,19 @@ def get_presence_gcf_strain(gcfs: Sequence[GCF], strains: StrainCollection) -> p
     """Get the occurence of strains in gcfs.
 
     The occurence is a DataFrame with gcfs as rows and strains as columns,
-    where index is `gcf.gcf_id` and column name is `strain.id`. The values
+    where index is `gcf.id` and column name is `strain.id`. The values
     are 1 if the gcf contains the strain and 0 otherwise.
     """
     df_gcf_strain = pd.DataFrame(
         np.zeros((len(gcfs), len(strains))),
-        index=[gcf.gcf_id for gcf in gcfs],
+        index=[gcf.id for gcf in gcfs],
         columns=[strain.id for strain in strains],
         dtype=int,
     )
     for gcf in gcfs:
         for strain in strains:
             if gcf.has_strain(strain):
-                df_gcf_strain.loc[gcf.gcf_id, strain.id] = 1
+                df_gcf_strain.loc[gcf.id, strain.id] = 1
     return df_gcf_strain
 
 
@@ -43,19 +43,19 @@ def get_presence_spec_strain(
     """Get the occurence of strains in spectra.
 
     The occurence is a DataFrame with spectra as rows and strains as columns,
-    where index is `spectrum.spectrum_id` and column name is `strain.id`.
+    where index is `spectrum.id` and column name is `strain.id`.
     The values are 1 if the spectrum contains the strain and 0 otherwise.
     """
     df_spec_strain = pd.DataFrame(
         np.zeros((len(spectra), len(strains))),
-        index=[spectrum.spectrum_id for spectrum in spectra],
+        index=[spectrum.id for spectrum in spectra],
         columns=[strain.id for strain in strains],
         dtype=int,
     )
     for spectrum in spectra:
         for strain in strains:
             if spectrum.has_strain(strain):
-                df_spec_strain.loc[spectrum.spectrum_id, strain.id] = 1
+                df_spec_strain.loc[spectrum.id, strain.id] = 1
     return df_spec_strain
 
 
@@ -65,18 +65,18 @@ def get_presence_mf_strain(
     """Get the occurence of strains in molecular families.
 
     The occurence is a DataFrame with molecular families as rows and
-    strains as columns, where index is `mf.family_id` and column name is
+    strains as columns, where index is `mf.id` and column name is
     `strain.id`. The values are 1 if the molecular family contains the
     strain and 0 otherwise.
     """
     df_mf_strain = pd.DataFrame(
         np.zeros((len(mfs), len(strains))),
-        index=[mf.family_id for mf in mfs],
+        index=[mf.id for mf in mfs],
         columns=[strain.id for strain in strains],
         dtype=int,
     )
     for mf in mfs:
         for strain in strains:
             if mf.has_strain(strain):
-                df_mf_strain.loc[mf.family_id, strain.id] = 1
+                df_mf_strain.loc[mf.id, strain.id] = 1
     return df_mf_strain
diff --git a/src/nplinker/strain/strain.py b/src/nplinker/strain/strain.py
index 358ed371..20818f29 100644
--- a/src/nplinker/strain/strain.py
+++ b/src/nplinker/strain/strain.py
@@ -12,13 +12,13 @@ class Strain:
     id.
     """
 
-    def __init__(self, primary_id: str) -> None:
+    def __init__(self, id: str) -> None:
         """To model the mapping between strain id and its aliases.
 
         Args:
-            primary_id: the representative id of the strain.
+            id: the representative id of the strain.
         """
-        self.id: str = primary_id
+        self.id: str = id
         self._aliases: set[str] = set()
 
     def __repr__(self) -> str:
diff --git a/tests/unit/genomics/test_antismash_loader.py b/tests/unit/genomics/test_antismash_loader.py
index 2cee2b13..64f205aa 100644
--- a/tests/unit/genomics/test_antismash_loader.py
+++ b/tests/unit/genomics/test_antismash_loader.py
@@ -62,7 +62,7 @@ def test_parse_bgc_genbank():
     gbk_file = str(DATA_DIR / "antismash" / "GCF_000514515.1" / "NZ_AZWB01000005.region001.gbk")
     bgc = parse_bgc_genbank(gbk_file)
     assert isinstance(bgc, BGC)
-    assert bgc.bgc_id == "NZ_AZWB01000005.region001"
+    assert bgc.id == "NZ_AZWB01000005.region001"
     assert bgc.product_prediction == ("NRPS", "lanthipeptide")
     assert "Salinispora pacifica CNT029 B170DRAFT_scaffold" in bgc.description
     assert bgc.antismash_id == "NZ_AZWB01000005"
diff --git a/tests/unit/genomics/test_bgc.py b/tests/unit/genomics/test_bgc.py
index 9c0e6932..1cf3f401 100644
--- a/tests/unit/genomics/test_bgc.py
+++ b/tests/unit/genomics/test_bgc.py
@@ -5,7 +5,7 @@
 
 def test_default():
     bgc = BGC("BGC0000001", "Polyketide")
-    assert bgc.bgc_id == "BGC0000001"
+    assert bgc.id == "BGC0000001"
     assert bgc.product_prediction == ("Polyketide",)
     assert bgc.is_mibig() is True
     assert bgc.parents == set()
diff --git a/tests/unit/genomics/test_gcf.py b/tests/unit/genomics/test_gcf.py
index ded23e27..cd694472 100644
--- a/tests/unit/genomics/test_gcf.py
+++ b/tests/unit/genomics/test_gcf.py
@@ -23,7 +23,7 @@ def bgc_without_strain():
 def test_init():
     """Test the initialization of GCF."""
     gcf = GCF("1")
-    assert gcf.gcf_id == "1"
+    assert gcf.id == "1"
     assert gcf.bgcs == set()
     assert isinstance(gcf.strains, StrainCollection)
     assert len(gcf.strains) == 0
@@ -77,7 +77,7 @@ def test_add_bgc_wo_strain(bgc_without_strain, caplog):
     """Test add_bgc method with a BGC that does have strain."""
     gcf = GCF("1")
     gcf.add_bgc(bgc_without_strain)
-    assert gcf.gcf_id == "1"
+    assert gcf.id == "1"
     assert gcf.bgcs == {bgc_without_strain}
     assert len(gcf.strains) == 0
     assert "No strain specified for the BGC" in caplog.text
diff --git a/tests/unit/genomics/test_mibig_loader.py b/tests/unit/genomics/test_mibig_loader.py
index 0cb59103..1188971b 100644
--- a/tests/unit/genomics/test_mibig_loader.py
+++ b/tests/unit/genomics/test_mibig_loader.py
@@ -67,5 +67,5 @@ def test_parse_bgc_metadata_json():
     json_file = DATA_DIR / "mibig" / "BGC0000001_v3.1.json"
     bgc = parse_bgc_metadata_json(str(json_file))
     assert isinstance(bgc, BGC)
-    assert bgc.bgc_id == "BGC0000001"
+    assert bgc.id == "BGC0000001"
     assert bgc.mibig_bgc_class == ("Polyketide",)
diff --git a/tests/unit/metabolomics/test_gnps_molecular_family_loader.py b/tests/unit/metabolomics/test_gnps_molecular_family_loader.py
index 9f3ad4f3..99dd3f1a 100644
--- a/tests/unit/metabolomics/test_gnps_molecular_family_loader.py
+++ b/tests/unit/metabolomics/test_gnps_molecular_family_loader.py
@@ -22,5 +22,5 @@ def test_gnps_molecular_family_loader(
     actual = loader.get_mfs(keep_singleton=keep_singleton)
     assert len(actual) == num_families
     # test molecular family with id "1" has correct number of spectra ids
-    mf = [mf for mf in actual if mf.family_id == "1"][0]
+    mf = [mf for mf in actual if mf.id == "1"][0]
     assert len(mf.spectra_ids) == num_spectra
diff --git a/tests/unit/metabolomics/test_molecular_family.py b/tests/unit/metabolomics/test_molecular_family.py
index 7713e189..eb6fcd26 100644
--- a/tests/unit/metabolomics/test_molecular_family.py
+++ b/tests/unit/metabolomics/test_molecular_family.py
@@ -8,7 +8,7 @@
 @pytest.fixture()
 def spectrum1():
     """Return a Spectrum object."""
-    spec = Spectrum(spectrum_id="spec001", mz=[1.0], intensity=[1.0], precursor_mz=100.0)
+    spec = Spectrum(id="spec001", mz=[1.0], intensity=[1.0], precursor_mz=100.0)
     spec.strains = StrainCollection()
     spec.strains.add(Strain("strain001"))
     yield spec
@@ -17,7 +17,7 @@ def spectrum1():
 @pytest.fixture()
 def spectrum2():
     """Return a Spectrum object."""
-    spec = Spectrum(spectrum_id="spec002", mz=[1.0], intensity=[1.0], precursor_mz=100.0)
+    spec = Spectrum(id="spec002", mz=[1.0], intensity=[1.0], precursor_mz=100.0)
     spec.strains = StrainCollection()
     spec.strains.add(Strain("strain002"))
     yield spec
@@ -26,7 +26,7 @@ def spectrum2():
 def test_init():
     """Test MolecularFamily class initialization."""
     mf = MolecularFamily("mf001")
-    assert mf.family_id == "mf001"
+    assert mf.id == "mf001"
     assert mf.spectra_ids == set()
     assert mf.spectra == set()
     assert mf.strains == StrainCollection()
@@ -35,10 +35,7 @@ def test_init():
 def test_str_repr():
     """Test __str__ and __repr__ methods."""
     mf = MolecularFamily("mf001")
-    assert (
-        str(mf)
-        == "MolecularFamily(family_id=mf001, #Spectrum_objects=0, #spectrum_ids=0, #strains=0)"
-    )
+    assert str(mf) == "MolecularFamily(id=mf001, #Spectrum_objects=0, #spectrum_ids=0, #strains=0)"
     assert repr(mf) == str(mf)
 
 
@@ -80,11 +77,11 @@ def test_add_spectrum(spectrum1, spectrum2):
     mf = MolecularFamily("mf001")
     mf.add_spectrum(spectrum1)
     assert spectrum1 in mf.spectra
-    assert spectrum1.spectrum_id in mf.spectra_ids
+    assert spectrum1.id in mf.spectra_ids
     assert Strain("strain001") in mf.strains
     mf.add_spectrum(spectrum2)
     assert spectrum2 in mf.spectra
-    assert spectrum2.spectrum_id in mf.spectra_ids
+    assert spectrum2.id in mf.spectra_ids
     assert Strain("strain002") in mf.strains
     assert len(mf.spectra) == 2
     assert len(mf.spectra_ids) == 2
@@ -98,12 +95,12 @@ def test_detach_spectrum(spectrum1, spectrum2):
     mf.add_spectrum(spectrum2)
     mf.detach_spectrum(spectrum1)
     assert spectrum1 not in mf.spectra
-    assert spectrum1.spectrum_id not in mf.spectra_ids
+    assert spectrum1.id not in mf.spectra_ids
     assert Strain("strain001") not in mf.strains
     assert Strain("strain002") in mf.strains
     mf.detach_spectrum(spectrum2)
     assert spectrum2 not in mf.spectra
-    assert spectrum2.spectrum_id not in mf.spectra_ids
+    assert spectrum2.id not in mf.spectra_ids
     assert Strain("strain002") not in mf.strains
     assert len(mf.spectra) == 0
     assert len(mf.spectra_ids) == 0
diff --git a/tests/unit/metabolomics/test_spectrum.py b/tests/unit/metabolomics/test_spectrum.py
index 3c4d22ed..e984eaba 100644
--- a/tests/unit/metabolomics/test_spectrum.py
+++ b/tests/unit/metabolomics/test_spectrum.py
@@ -16,7 +16,7 @@ def test_init(rt, metadata, expected_metadata):
     """Test the initialization of the Spectrum class."""
     spec = Spectrum("spec1", [100, 200], [0.1, 0.2], 150, rt, metadata)
 
-    assert spec.spectrum_id == "spec1"
+    assert spec.id == "spec1"
     assert spec.mz == [100, 200]
     assert spec.intensity == [0.1, 0.2]
     assert spec.precursor_mz == 150
@@ -33,8 +33,8 @@ def test_init(rt, metadata, expected_metadata):
 def test_str_repr():
     """Test the __str__ and __repr__ methods."""
     spec = Spectrum("spec1", [100, 200], [0.1, 0.2], 150)
-    assert str(spec) == "Spectrum(spectrum_id=spec1, #strains=0)"
-    assert repr(spec) == "Spectrum(spectrum_id=spec1, #strains=0)"
+    assert str(spec) == "Spectrum(id=spec1, #strains=0)"
+    assert repr(spec) == "Spectrum(id=spec1, #strains=0)"
 
 
 def test_eq():
diff --git a/tests/unit/scoring/conftest.py b/tests/unit/scoring/conftest.py
index bea4edb3..cb750407 100644
--- a/tests/unit/scoring/conftest.py
+++ b/tests/unit/scoring/conftest.py
@@ -77,9 +77,9 @@ def npl(gcfs, spectra, mfs, strains, tmp_path) -> NPLinker:
     npl._spectra = spectra
     npl._molfams = mfs
     npl._strains = strains
-    npl._gcf_lookup = {gcf.gcf_id: gcf for gcf in gcfs}
-    npl._mf_lookup = {mf.family_id: mf for mf in mfs}
-    npl._spec_lookup = {spec.spectrum_id: spec for spec in spectra}
+    npl._gcf_lookup = {gcf.id: gcf for gcf in gcfs}
+    npl._mf_lookup = {mf.id: mf for mf in mfs}
+    npl._spec_lookup = {spec.id: spec for spec in spectra}
     return npl
 
 
diff --git a/tests/unit/scoring/test_nplinker_scoring.py b/tests/unit/scoring/test_nplinker_scoring.py
index a76c2231..3b65f911 100644
--- a/tests/unit/scoring/test_nplinker_scoring.py
+++ b/tests/unit/scoring/test_nplinker_scoring.py
@@ -16,7 +16,7 @@ def test_get_links_gcf_standardised_false(npl, mc, gcfs, spectra, mfs, strains_l
     assert isinstance(links, LinkCollection)
     links = links.links  # dict of link values
     assert len(links) == 3
-    assert {i.gcf_id for i in links.keys()} == {"gcf1", "gcf2", "gcf3"}
+    assert {i.id for i in links.keys()} == {"gcf1", "gcf2", "gcf3"}
     assert isinstance(links[gcfs[0]][spectra[0]], ObjectLink)
     assert links[gcfs[0]][spectra[0]].data(mc) == 12
     assert links[gcfs[1]][spectra[0]].data(mc) == -9
@@ -30,7 +30,7 @@ def test_get_links_gcf_standardised_false(npl, mc, gcfs, spectra, mfs, strains_l
     links = npl.get_links(list(gcfs), mc, and_mode=True)
     assert isinstance(links, LinkCollection)
     links = links.links
-    assert {i.gcf_id for i in links.keys()} == {"gcf1", "gcf2", "gcf3"}
+    assert {i.id for i in links.keys()} == {"gcf1", "gcf2", "gcf3"}
     assert isinstance(links[gcfs[0]][spectra[0]], ObjectLink)
     # test scores
     assert links[gcfs[0]][spectra[0]].data(mc) == 12
@@ -57,7 +57,7 @@ def test_get_links_spec_standardised_false(npl, mc, gcfs, spectra, strains_list)
     assert isinstance(links, LinkCollection)
     links = links.links  # dict of link values
     assert len(links) == 3
-    assert {i.spectrum_id for i in links.keys()} == {"spectrum1", "spectrum2", "spectrum3"}
+    assert {i.id for i in links.keys()} == {"spectrum1", "spectrum2", "spectrum3"}
     assert isinstance(links[spectra[0]][gcfs[0]], ObjectLink)
     assert links[spectra[0]][gcfs[0]].data(mc) == 12
     assert links[spectra[0]][gcfs[1]].data(mc) == -9
@@ -68,7 +68,7 @@ def test_get_links_spec_standardised_false(npl, mc, gcfs, spectra, strains_list)
     assert isinstance(links, LinkCollection)
     links = links.links  # dict of link values
     assert len(links) == 3
-    assert {i.spectrum_id for i in links.keys()} == {"spectrum1", "spectrum2", "spectrum3"}
+    assert {i.id for i in links.keys()} == {"spectrum1", "spectrum2", "spectrum3"}
     assert isinstance(links[spectra[0]][gcfs[0]], ObjectLink)
     assert links[spectra[0]][gcfs[0]].data(mc) == 12
     assert links[spectra[0]].get(gcfs[1]) is None
@@ -91,7 +91,7 @@ def test_get_links_mf_standardised_false(npl, mc, gcfs, mfs, strains_list):
     assert isinstance(links, LinkCollection)
     links = links.links
     assert len(links) == 3
-    assert {i.family_id for i in links.keys()} == {"mf1", "mf2", "mf3"}
+    assert {i.id for i in links.keys()} == {"mf1", "mf2", "mf3"}
     assert isinstance(links[mfs[0]][gcfs[0]], ObjectLink)
     assert links[mfs[0]][gcfs[0]].data(mc) == 12
     assert links[mfs[0]][gcfs[1]].data(mc) == -9
@@ -102,7 +102,7 @@ def test_get_links_mf_standardised_false(npl, mc, gcfs, mfs, strains_list):
     assert isinstance(links, LinkCollection)
     links = links.links
     assert len(links) == 3
-    assert {i.family_id for i in links.keys()} == {"mf1", "mf2", "mf3"}
+    assert {i.id for i in links.keys()} == {"mf1", "mf2", "mf3"}
     assert isinstance(links[mfs[0]][gcfs[0]], ObjectLink)
     assert links[mfs[0]][gcfs[0]].data(mc) == 12
     assert links[mfs[0]].get(gcfs[1]) is None