diff --git a/Project.toml b/Project.toml
index 4121522..d4520f0 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "FBCModelTests"
 uuid = "1060cd45-1c33-4a14-be81-8fa38fdd82bf"
 authors = ["The developers of FBCModelTests.jl"]
-version = "0.2.5"
+version = "0.3.0"
 
 [deps]
 COBREXA = "babc4406-5200-4a30-9033-bf5ae714c842"
diff --git a/src/memote/checks/Annotation.jl b/src/memote/checks/Annotation.jl
index 2d6dd1b..aa9be13 100644
--- a/src/memote/checks/Annotation.jl
+++ b/src/memote/checks/Annotation.jl
@@ -19,20 +19,20 @@ is_annotated_gene(model, gid) = !isempty(gene_annotations(model, gid))
 """
 $(TYPEDSIGNATURES)
 
-Helper function to find all the annotations that are missing for a component in a model.
+Helper function to find all the annotations for a component in a model.
 """
-function _find_unannotated_components(
+function _find_annotated_components(
     model::MetabolicModel,
     id_accessor::String,
     annotation_accessor,
     annotation_kws,
 )
-    missing_annos = String[]
+    found_annos = String[]
     for anno_kw in annotation_kws
         annos = parse_annotations(annotation_accessor(model, id_accessor))
-        !haskey(annos, anno_kw) && push!(missing_annos, anno_kw)
+        haskey(annos, anno_kw) && push!(found_annos, anno_kw)
     end
-    return missing_annos
+    return found_annos
 end
 
 """
@@ -40,10 +40,10 @@ $(TYPEDSIGNATURES)
 
 Checks if the databases listed in `config.annotation.gene_annotation_keywords`
 are present in the gene annotations. Returns a vector of annotation keywords
-that were not found.
+that were found.
 """
-findall_unannotated_gene_databases(model, gid::String; config = Config.memote_config) =
-    _find_unannotated_components(
+findall_annotated_gene_databases(model, gid::String; config = Config.memote_config) =
+    _find_annotated_components(
         model,
         gid,
         gene_annotations,
@@ -55,28 +55,25 @@ $(TYPEDSIGNATURES)
 
 Checks if the databases listed in `config.annotation.metabolite_annotation_keywords`
 are present in the metabolite annotations. Returns a vector of annotation keywords
-that were not found.
+that were found.
 """
-findall_unannotated_metabolite_databases(
-    model,
-    mid::String;
-    config = Config.memote_config,
-) = _find_unannotated_components(
-    model,
-    mid,
-    metabolite_annotations,
-    config.annotation.metabolite_annotation_keywords,
-)
+findall_annotated_metabolite_databases(model, mid::String; config = Config.memote_config) =
+    _find_annotated_components(
+        model,
+        mid,
+        metabolite_annotations,
+        config.annotation.metabolite_annotation_keywords,
+    )
 
 """
 $(TYPEDSIGNATURES)
 
 Checks if the databases listed in `config.annotation.reaction_annotation_keywords`
 are present in the reaction annotations. Returns a vector of annotation keywords
-that were not found.
+that were found.
 """
-findall_unannotated_reaction_databases(model, rid::String; config = Config.memote_config) =
-    _find_unannotated_components(
+findall_annotated_reaction_databases(model, rid::String; config = Config.memote_config) =
+    _find_annotated_components(
         model,
         rid,
         reaction_annotations,
@@ -86,23 +83,24 @@ findall_unannotated_reaction_databases(model, rid::String; config = Config.memot
 """
 $(TYPEDSIGNATURES)
 
-Helper function to find all the annotations for a component that do not conform in the model.
+Helper function to find all the annotations for a component that conform to
+recognized patterns in the model.
 """
-function _find_nonconformal_annotations(
+function _find_conformal_annotations(
     model::MetabolicModel,
     id_accessor::String,
     annotation_accessor,
     annotation_regex,
 )
-    no_annos = String[]
+    conform_annos = String[]
     for (anno_kw, anno_regex) in annotation_regex
         annos = parse_annotations(annotation_accessor(model, id_accessor))
         if haskey(annos, anno_kw)
-            in.(nothing, Ref(match.(anno_regex, annos[anno_kw]))) &&
-                push!(no_annos, anno_kw)
+            in.(nothing, Ref(match.(anno_regex, annos[anno_kw]))) ||
+                push!(conform_annos, anno_kw)
         end
     end
-    return no_annos
+    return conform_annos
 end
 
 """
@@ -111,10 +109,10 @@ $(TYPEDSIGNATURES)
 Check if the gene annotation entry conforms to commonly recognized formats of
 annotation database using regex patterns. Uses the database formats listed in
 `config.annotation.gene_annotation_regexes` to test the conformity. Returns a
-string vector of database ids do not conform.
+string vector of database ids that do conform.
 """
-findall_nonconformal_gene_annotations(model, gid::String; config = Config.memote_config) =
-    _find_nonconformal_annotations(
+findall_conformal_gene_annotations(model, gid::String; config = Config.memote_config) =
+    _find_conformal_annotations(
         model,
         gid,
         gene_annotations,
@@ -127,13 +125,13 @@ $(TYPEDSIGNATURES)
 Check if the metabolite annotation entry conforms to commonly recognized formats
 of annotation database using regex patterns. Uses the database formats listed in
 `config.annotation.metabolite_annotation_regexes` to test the conformity.
-Returns a string vector of database ids do not conform.
+Returns a string vector of database ids that do conform.
 """
-findall_nonconformal_metabolite_annotations(
+findall_conformal_metabolite_annotations(
     model,
     mid::String;
     config = Config.memote_config,
-) = _find_nonconformal_annotations(
+) = _find_conformal_annotations(
     model,
     mid,
     metabolite_annotations,
@@ -146,17 +144,14 @@ $(TYPEDSIGNATURES)
 Check if the reaction annotation entry conforms to commonly recognized formats
 of annotation database using regex patterns. Uses the database formats listed in
 `config.annotation.reaction_annotation_regexes` to test the conformity. Returns
-a string vector of database ids do not conform.
+a string vector of database ids that do conform.
 """
-findall_nonconformal_reaction_annotations(
-    model,
-    rid::String;
-    config = Config.memote_config,
-) = _find_nonconformal_annotations(
-    model,
-    rid,
-    reaction_annotations,
-    config.annotation.reaction_annotation_regexes,
-)
+findall_conformal_reaction_annotations(model, rid::String; config = Config.memote_config) =
+    _find_conformal_annotations(
+        model,
+        rid,
+        reaction_annotations,
+        config.annotation.reaction_annotation_regexes,
+    )
 
 end # module
diff --git a/src/memote/checks/Metabolites.jl b/src/memote/checks/Metabolites.jl
index 3a7bb01..a2757f8 100644
--- a/src/memote/checks/Metabolites.jl
+++ b/src/memote/checks/Metabolites.jl
@@ -18,33 +18,24 @@ $(TYPEDSIGNATURES)
 Test if metabolites `m1` and `m2` are different by comparing their
 `config.metabolite.test_annotation` field in the annotations of each
 metabolite. Note, if no annotations are present for one or both of the
-metabolites, then return `true`.
+metabolites, then return `false`.
 """
-function metabolites_are_duplicated(
-    model::MetabolicModel,
-    m1,
-    m2;
-    config = Config.memote_config,
-)
-    k1s = get(
-        parse_annotations(metabolite_annotations(model, m1)),
-        config.metabolite.test_annotation,
-        nothing,
-    )
-    isnothing(k1s) && return true
-    k2s = get(
-        parse_annotations(metabolite_annotations(model, m2)),
-        config.metabolite.test_annotation,
-        nothing,
-    )
-    isnothing(k2s) && return true
+function metabolites_are_duplicated(model::MetabolicModel, m1, m2, test_annotation)
+    k1s =
+        get(parse_annotations(metabolite_annotations(model, m1)), test_annotation, nothing)
+    isnothing(k1s) && return false
+    k2s =
+        get(parse_annotations(metabolite_annotations(model, m2)), test_annotation, nothing)
+    isnothing(k2s) && return false
     any(in.(k1s, Ref(k2s)))
 end
 
 """
 $(TYPEDSIGNATURES)
 
-Return a dictionary of metabolites that are duplicated in their compartment.
+Return a dictionary of metabolites that are duplicated in their compartment. If
+any of the test annotations, stored in `config.metabolite.test_annotations`, are
+repeated, then the metabolite is counted as duplicated. Missing annotations are ignored.
 """
 function metabolites_duplicated_in_compartment(
     model::MetabolicModel;
@@ -55,7 +46,12 @@ function metabolites_duplicated_in_compartment(
         c1 = metabolite_compartment(model, m1)
         for m2 in metabolites(model)
             c2 = metabolite_compartment(model, m2)
-            if c1 == c2 && m1 != m2 && metabolites_are_duplicated(model, m1, m2; config)
+            if c1 == c2 &&
+               m1 != m2 &&
+               any(
+                   metabolites_are_duplicated(model, m1, m2, test_annotation) for
+                   test_annotation in config.metabolite.test_annotations
+               )
                 push!(unique_metabolites, m1)
             end
         end
@@ -66,28 +62,34 @@ end
 """
 $(TYPEDSIGNATURES)
 
-Helper function to find orphan or deadend metabolites. Specify `consumed=true`
-to consider orphan metabolites or `false` to consider deadend metabolites. Set
-`complete_medium=true` to open all boundary reactions to simulate a complete
-medium.
+Helper function to find orphan or deadend metabolites. Specify
+`only_consumed=true` to consider orphan metabolites or `false` to consider
+deadend metabolites.
 """
-function _find_orphan_or_deadend_metabolites(model::MetabolicModel; consumed = true)
+function _find_orphan_or_deadend_metabolites(model::MetabolicModel; only_consumed = true)
     mids = metabolites(model)
+    rids = reactions(model)
     mets = String[]
     S = stoichiometry(model)
     lbs, ubs = bounds(model)
     for idx in axes(S, 1)
-        rids, vals = findnz(S[idx, :])
-        if length(vals) == 1 && (consumed ? first(vals) < 0 : first(vals) > 0)
-            ridx = first(rids)
-            rid = reactions(model)[ridx]
-            met = mids[idx]
-            v = reaction_stoichiometry(model, rid)[met]
-            # check if reaction can actually make or consume the metabolite
-            lbs[ridx] < 0 < ubs[ridx] && continue # ignore reversible reactions
-            consumed && lbs[ridx] * v <= 0 && push!(mets, met)
-            !consumed && ubs[ridx] * v >= 0 && push!(mets, met)
+        mid = mids[idx]
+        one_sided_metabolite = true
+        for (ridx, _) in zip(findnz(S[idx, :])...)
+            lbs[ridx] < 0 < ubs[ridx] && (one_sided_metabolite = false; break) # can be produced or consumed
+            rid = rids[ridx]
+            rs = reaction_stoichiometry(model, rid)[mid]
+            if only_consumed # consumed only
+                (rs < 0 && lbs[ridx] >= 0) ||
+                    (rs > 0 && ubs[ridx] <= 0) ||
+                    (one_sided_metabolite = false; break)
+            else # produced only
+                (rs > 0 && lbs[ridx] >= 0) ||
+                    (rs < 0 && ubs[ridx] <= 0) ||
+                    (one_sided_metabolite = false; break)
+            end
         end
+        one_sided_metabolite && push!(mets, mid)
     end
     return mets
 end
@@ -96,20 +98,19 @@ end
 $(TYPEDSIGNATURES)
 
 Find all metabolites that can only (excludes reversible reactions) be consumed
-in the `model` by inspecting the stoichiometric matrix.
+in the `model` by inspecting the stoichiometric matrix and reaction bounds.
 """
 find_orphan_metabolites(model::MetabolicModel) =
-    _find_orphan_or_deadend_metabolites(model, consumed = true)
+    _find_orphan_or_deadend_metabolites(model, only_consumed = true)
 
 """
 $(TYPEDSIGNATURES)
 
 Find all metabolites that can only (excludes reversible reactions) be produced
-in the `model` by inspecting the stoichiometric matrix.
+in the `model` by inspecting the stoichiometric matrix and reaction bounds.
 """
 find_deadend_metabolites(model::MetabolicModel) =
-    _find_orphan_or_deadend_metabolites(model, consumed = false)
-
+    _find_orphan_or_deadend_metabolites(model, only_consumed = false)
 
 """
 $(TYPEDSIGNATURES)
@@ -119,5 +120,4 @@ Returns a list of all metabolites that aren't part of any reactions.
 find_disconnected_metabolites(model::MetabolicModel) =
     metabolites(model)[all(stoichiometry(model) .== 0, dims = 2)[:]]
 
-
 end # module
diff --git a/src/memote/checks/Network.jl b/src/memote/checks/Network.jl
index baec31d..770158c 100644
--- a/src/memote/checks/Network.jl
+++ b/src/memote/checks/Network.jl
@@ -108,7 +108,7 @@ function find_all_universally_blocked_reactions(
 
     fvas = flux_variability_analysis(
         stdmodel,
-        collect(1:n_reactions(model)),
+        collect(1:n_reactions(stdmodel)),
         optimizer;
         modifications = config.network.optimizer_modifications,
         workers,
@@ -121,7 +121,7 @@ function find_all_universally_blocked_reactions(
         isnothing(vs[2]) && continue
         abs(vs[1]) <= config.network.blocked_tol &&
             abs(vs[2]) <= config.network.blocked_tol &&
-            (push!(blocked_rxns, rid); break)
+            push!(blocked_rxns, rid)
     end
 
     blocked_rxns
diff --git a/src/memote/config.jl b/src/memote/config.jl
index 1b446cb..62ab659 100644
--- a/src/memote/config.jl
+++ b/src/memote/config.jl
@@ -108,8 +108,8 @@ Base.@kwdef mutable struct AnnotationConfig
     metabolite_annotation_regexes::Dict{String,Regex}
     reaction_annotation_keywords::Vector{String}
     reaction_annotation_regexes::Dict{String,Regex}
-    maximum_nonconformal_references::Int64
-    maximum_missing_databases::Int64
+    minimum_conformal_crossreferences::Int64
+    minimum_crossreferences::Int64
 end
 
 annotation_config = AnnotationConfig(
@@ -190,8 +190,8 @@ annotation_config = AnnotationConfig(
             r"^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$",
         "biocyc" => r"^[A-Z-0-9]+(?<!CHEBI)(\:)?[A-Za-z0-9+_.%-]+$",
     ),
-    maximum_nonconformal_references = 5,
-    maximum_missing_databases = 6,
+    minimum_conformal_crossreferences = 3,
+    minimum_crossreferences = 4,
 )
 
 """
@@ -319,10 +319,11 @@ $(TYPEDEF)
 $(TYPEDFIELDS)
 """
 Base.@kwdef mutable struct MetaboliteConfig
-    test_annotation::String
+    test_annotations::Vector{String}
 end
 
-metabolite_config = MetaboliteConfig(test_annotation = "inchi_key")
+metabolite_config =
+    MetaboliteConfig(test_annotations = ["inchi_key", "chebi", "metanetx.chemical"])
 
 """
 $(TYPEDEF)
@@ -340,7 +341,7 @@ end
 network_config = NetworkConfig(
     condition_number = 1e9,
     cycle_tol = 1e-3,
-    blocked_tol = 1e-3,
+    blocked_tol = 1e-8,
     optimizer_modifications = [silence],
 )
 
diff --git a/src/memote/frontend.jl b/src/memote/frontend.jl
index 1047e2c..68d868a 100644
--- a/src/memote/frontend.jl
+++ b/src/memote/frontend.jl
@@ -13,7 +13,7 @@ function run_tests_toplevel(
     filename = nothing,
     workers = [myid()],
 )
-    @testset QuietTestSet "Memote" begin
+    @testset QuietTestSet "Memote.jl" begin
         run_tests(model, optimizer; config, workers, filename)
     end
 end
@@ -62,54 +62,67 @@ function run_tests(
     @testset "Metabolic Model Tests$(isnothing(filename) ? "" : ": $filename")" begin
         @info "Testing basic information about the model..."
         @testset "Basic information" begin
-            @atest Basic.model_has_reactions(model) "The model has reactions."
-            @atest Basic.model_has_metabolites(model) "The model has metabolites."
-            @atest Basic.model_has_genes(model) "The model has genes."
-            @atest Basic.model_has_compartments(model) "The model has at least 1 comparment."
+            @atest Basic.model_has_reactions(model) "The model has reactions"
+            @atest Basic.model_has_metabolites(model) "The model has metabolites"
+            @atest Basic.model_has_genes(model) "The model has genes"
+            @atest Basic.model_has_compartments(model) "The model has at least 1 comparment"
             metcov = Basic.model_metabolic_coverage(model)
-            @atest config.basic.minimum_metabolic_coverage <= metcov "The metabolic coverage of the model is $(round(metcov, digits=2)), but it should be bigger than $(round(config.basic.minimum_metabolic_coverage, digits=2)) to pass."
-            @atest Basic.model_solves_in_default_medium(model, optimizer; config) "The model solves in the default medium with an objective value within [$(round(config.basic.minimum_growth_rate, digits=2)), $(round(config.basic.maximum_growth_rate,digits=2))]."
+            @atest config.basic.minimum_metabolic_coverage <= metcov "The metabolic coverage of the model is $(round(metcov, digits=2)), but it should be bigger than $(round(config.basic.minimum_metabolic_coverage, digits=2)) to pass"
+            @atest Basic.model_solves_in_default_medium(model, optimizer; config) "The model solves in the default medium with an objective value within [$(round(config.basic.minimum_growth_rate, digits=2)), $(round(config.basic.maximum_growth_rate,digits=2))]"
         end
 
         @info "Testing the model annotations..."
         @testset "Annotations" begin
             @testset "SBO annotations" begin
-                @atest any(is_metabolic_reaction(model, rid) for rid in reactions(model)) "At least 1 reaction is SBO annotated as a metabolic reaction."
-                @atest any(is_transport_reaction(model, rid) for rid in reactions(model)) "At least 1 reaction is SBO annotated as a transport reaction."
-                @atest any(is_biomass_reaction(model, rid) for rid in reactions(model)) "At least 1 reaction is SBO annotated as a biomass reaction."
-                @atest any(is_exchange_reaction(model, rid) for rid in reactions(model)) "At least 1 reaction is SBO annotated as an exchange reaction."
+                @atest any(is_metabolic_reaction(model, rid) for rid in reactions(model)) "At least 1 reaction is SBO annotated as a metabolic reaction"
+                @atest any(is_transport_reaction(model, rid) for rid in reactions(model)) "At least 1 reaction is SBO annotated as a transport reaction"
+                @atest any(is_biomass_reaction(model, rid) for rid in reactions(model)) "At least 1 reaction is SBO annotated as a biomass reaction"
+                @atest any(is_exchange_reaction(model, rid) for rid in reactions(model)) "At least 1 reaction is SBO annotated as an exchange reaction"
                 @atest any(
                     is_atp_maintenance_reaction(model, rid) for rid in reactions(model)
-                ) "At least 1 reaction is SBO annotated as an ATP maintenance reaction."
+                ) "At least 1 reaction is SBO annotated as an ATP maintenance reaction"
+                for rid in reactions(model)
+                    @atest any(
+                        in.(
+                            keys(
+                                Memote.Utils.parse_annotations(
+                                    reaction_annotations(model, rid),
+                                ),
+                            ),
+                            Ref(["sbo", "SBO"]),
+                        ),
+                    ) "$rid has an SBO annotation"
+                end
             end
 
             @testset "Reactions" begin
                 @testset "Any annotations present" begin
                     for rid in reactions(model)
-                        @atest Annotation.is_annotated_reaction(model, rid) "$rid has at least 1 annotation."
+                        @atest Annotation.is_annotated_reaction(model, rid) "$rid has at least 1 annotation"
                     end
                 end
 
-                @testset "At most $(config.annotation.maximum_missing_databases) missing cross-references per entry." begin
+                @testset "At least $(config.annotation.minimum_crossreferences) cross-references per entry" begin
                     for rid in reactions(model)
-                        @atest length(
-                            Annotation.findall_unannotated_reaction_databases(
+                        @atest config.annotation.minimum_crossreferences <= length(
+                            Annotation.findall_annotated_reaction_databases(
                                 model,
                                 rid;
                                 config,
                             ),
-                        ) <= config.annotation.maximum_missing_databases "$rid needs at least $(config.annotation.maximum_missing_databases) cross-references."
+                        ) "$rid needs at least $(config.annotation.minimum_crossreferences) cross-references"
                     end
                 end
-                @testset "At most $(config.annotation.maximum_nonconformal_references) unrecognizable cross-references per entry" begin
+                @testset "At least $(config.annotation.minimum_conformal_crossreferences) recognizable cross-references per entry" begin
                     for rid in reactions(model)
-                        @atest length(
-                            Annotation.findall_nonconformal_reaction_annotations(
+                        @atest config.annotation.minimum_conformal_crossreferences <=
+                               length(
+                            Annotation.findall_conformal_reaction_annotations(
                                 model,
                                 rid;
                                 config,
                             ),
-                        ) <= config.annotation.maximum_nonconformal_references "$rid needs at least $(config.annotation.maximum_nonconformal_references) recognizable cross-references."
+                        ) "$rid needs at least $(config.annotation.minimum_conformal_crossreferences) recognizable cross-references"
                     end
                 end
             end
@@ -117,91 +130,88 @@ function run_tests(
             @testset "Metabolites" begin
                 @testset "Any annotations present" begin
                     for mid in metabolites(model)
-                        @atest Annotation.is_annotated_metabolite(model, mid) "$mid has at least 1 annotation."
+                        @atest Annotation.is_annotated_metabolite(model, mid) "$mid has at least 1 annotation"
                     end
                 end
 
-                @testset "At most $(config.annotation.maximum_missing_databases) missing cross-references per entry" begin
+                @testset "At least $(config.annotation.minimum_crossreferences) cross-references per entry" begin
                     for mid in metabolites(model)
-                        @atest length(
-                            Annotation.findall_unannotated_metabolite_databases(
+                        @atest config.annotation.minimum_crossreferences <= length(
+                            Annotation.findall_annotated_metabolite_databases(
                                 model,
                                 mid;
                                 config,
                             ),
-                        ) <= config.annotation.maximum_missing_databases "$mid dneeds at least $(config.annotation.maximum_missing_databases) cross-references."
+                        ) "$mid dneeds at least $(config.annotation.minimum_crossreferences) cross-references"
                     end
                 end
-                @testset "At most $(config.annotation.maximum_nonconformal_references) unrecognizable cross-references per entry" begin
+                @testset "At least $(config.annotation.minimum_conformal_crossreferences) recognizable cross-references per entry" begin
                     for mid in metabolites(model)
-                        @atest length(
-                            Annotation.findall_nonconformal_metabolite_annotations(
+                        @atest config.annotation.minimum_conformal_crossreferences <=
+                               length(
+                            Annotation.findall_conformal_metabolite_annotations(
                                 model,
                                 mid;
                                 config,
                             ),
-                        ) <= config.annotation.maximum_nonconformal_references "$mid needs at least $(config.annotation.maximum_nonconformal_references) recognizable cross-references."
+                        ) "$mid needs at least $(config.annotation.minimum_conformal_crossreferences) recognizable cross-references"
                     end
                 end
             end
 
-
             @testset "Genes" begin
                 @testset "Any annotations present" begin
                     for gid in genes(model)
-                        @atest Annotation.is_annotated_gene(model, gid) "$gid has at least 1 annotation."
+                        @atest Annotation.is_annotated_gene(model, gid) "$gid has at least 1 annotation"
                     end
                 end
 
-                @testset "At most $(config.annotation.maximum_missing_databases) missing cross-references per entry" begin
+                @testset "At least $(config.annotation.minimum_crossreferences) cross-references per entry" begin
                     for gid in genes(model)
-                        @atest length(
-                            Annotation.findall_unannotated_gene_databases(
-                                model,
-                                gid;
-                                config,
-                            ),
-                        ) <= config.annotation.maximum_missing_databases "$gid needs at least $(config.annotation.maximum_missing_databases) cross-references."
+                        @atest config.annotation.minimum_crossreferences <= length(
+                            Annotation.findall_annotated_gene_databases(model, gid; config),
+                        ) "$gid needs at least $(config.annotation.minimum_crossreferences) cross-references"
                     end
                 end
-                @testset "At most $(config.annotation.maximum_nonconformal_references) unrecognizable cross-references per entry" begin
+                @testset "At least $(config.annotation.minimum_conformal_crossreferences) recognizable cross-references per entry" begin
                     for gid in genes(model)
-                        @atest length(
-                            Annotation.findall_nonconformal_gene_annotations(
+                        @atest config.annotation.minimum_conformal_crossreferences <=
+                               length(
+                            Annotation.findall_conformal_gene_annotations(
                                 model,
                                 gid;
                                 config,
                             ),
-                        ) <= config.annotation.maximum_nonconformal_references "$gid needs at least $(config.annotation.maximum_nonconformal_references) recognizable cross-references."
+                        ) "$gid needs at least $(config.annotation.minimum_conformal_crossreferences) recognizable cross-references"
                     end
                 end
             end
         end
 
         @info "Testing the biomass function(s)..."
-        @testset "Biomass" begin
-            @atest length(Biomass.findall_biomass_reactions(model)) > 0 "At least 1 biomass reaction is in the model."
+        @testset "Biomass reaction(s)" begin
+            @atest length(Biomass.findall_biomass_reactions(model)) > 0 "At least 1 biomass reaction is in the model"
 
-            @testset "ATP burn included" begin
+            @testset "ATP + H2O -> ADP + Pi + H included" begin
                 for rid in Biomass.findall_biomass_reactions(model)
-                    @atest Biomass.atp_present_in_biomass_reaction(model, rid) "$rid (biomass reaction) hydrolyses ATP into ADP."
+                    @atest Biomass.atp_present_in_biomass_reaction(model, rid) "$rid (biomass reaction) hydrolyses ATP into ADP"
                 end
             end
             @testset "Molar mass consistent" begin
                 for rid in Biomass.findall_biomass_reactions(model)
-                    @atest Biomass.biomass_reaction_is_consistent(model, rid) "$rid (biomass reaction) is consistent."
+                    @atest Biomass.biomass_reaction_is_consistent(model, rid) "$rid (biomass reaction) is consistent"
                 end
             end
-            @testset "Missing common precursors" begin
+            @testset "Has all common precursors" begin
                 for rid in Biomass.findall_biomass_reactions(model)
-                    @atest Biomass.biomass_missing_essential_precursors(model, rid; config) "$rid (biomass reaction) contains all the common precursors."
+                    @atest Biomass.biomass_missing_essential_precursors(model, rid; config) "$rid (biomass reaction) contains all the common precursors"
                 end
             end
         end
 
         @info "Testing the stoichiometric consistency of the model..."
-        @testset "Stoichiometrically consistent" begin
-            @atest Consistency.model_is_consistent(model, optimizer; config) "The model is stoichiometrically consistent."
+        @testset "Stoichiometric consistency" begin
+            @atest Consistency.model_is_consistent(model, optimizer; config) "The model is stoichiometrically consistent"
         end
 
         @info "Testing the energy metabolism..."
@@ -219,17 +229,17 @@ function run_tests(
         @testset "GPR associations" begin
             @testset "Metabolic reactions have GPRs" begin
                 for rid in filter(x -> is_metabolic_reaction(model, x), reactions(model))
-                    @atest GPRAssociation.reaction_has_sensible_gpr(model, rid) "$rid (metabolic reaction) has at least 1 GPRs."
+                    @atest GPRAssociation.reaction_has_sensible_gpr(model, rid) "$rid (metabolic reaction) has at least 1 GPRs"
                 end
             end
 
             @testset "Transport reactions have GPRs" begin
                 for rid in filter(x -> is_transport_reaction(model, x), reactions(model))
-                    @atest GPRAssociation.reaction_has_sensible_gpr(model, rid) "$rid (transport reaction) has at least 1 GPRs."
+                    @atest GPRAssociation.reaction_has_sensible_gpr(model, rid) "$rid (transport reaction) has at least 1 GPRs"
                 end
             end
 
-            @atest length(GPRAssociation.reactions_with_complexes(model)) != 0 "At least 1 enzyme complex exists in the model."
+            @atest length(GPRAssociation.reactions_with_complexes(model)) != 0 "At least 1 enzyme complex exists in the model"
         end
 
         @info "Testing the reaction information..."
@@ -244,7 +254,7 @@ function run_tests(
                     if rid in config.reaction.charge_ignored_reactions
                         @test_skip Reactions.reaction_is_charge_balanced(model, rid)
                     else
-                        @atest Reactions.reaction_is_charge_balanced(model, rid) "$rid is charge balanced."
+                        @atest Reactions.reaction_is_charge_balanced(model, rid) "$rid is charge balanced"
                     end
                 end
             end
@@ -253,54 +263,54 @@ function run_tests(
                     if rid in config.reaction.mass_ignored_reactions
                         @test_skip Reactions.reaction_is_mass_balanced(model, rid)
                     else
-                        @atest Reactions.reaction_is_mass_balanced(model, rid) "$rid is mass balanced."
+                        @atest Reactions.reaction_is_mass_balanced(model, rid) "$rid is mass balanced"
                     end
                 end
             end
             @testset "No duplicated reactions" begin
                 dup_rxns = Reactions.findall_duplicated_reactions(model)
                 for rid in reactions(model)
-                    @atest rid ∉ dup_rxns "$rid is not duplicated."
+                    @atest rid ∉ dup_rxns "$rid is not duplicated"
                 end
             end
 
-            @atest Reactions.model_has_atpm_reaction(model) "There is an ATP maintenance reaction in the model."
+            @atest Reactions.model_has_atpm_reaction(model) "There is an ATP maintenance reaction in the model"
         end
 
         @info "Testing the metabolite information..."
         @testset "Metabolite information" begin
             @testset "No missing formulas" begin
                 for mid in metabolites(model)
-                    @atest !isnothing(metabolite_formula(model, mid)) "$mid has a formula."
+                    @atest !isnothing(metabolite_formula(model, mid)) "$mid has a formula"
                 end
             end
             @testset "No missing charges" begin
                 for mid in metabolites(model)
-                    @atest !isnothing(metabolite_charge(model, mid)) "$mid has a charge."
+                    @atest !isnothing(metabolite_charge(model, mid)) "$mid has a charge"
                 end
             end
-            @testset "Duplicated metabolites" begin
+            @testset "No duplicated metabolites" begin
                 dup_mids = Metabolites.metabolites_duplicated_in_compartment(model; config)
                 for mid in metabolites(model)
-                    @atest mid ∉ dup_mids "$mid is not duplicated."
+                    @atest mid ∉ dup_mids "$mid is not duplicated"
                 end
             end
             @testset "No orphan metabolites" begin
                 orphans = Metabolites.find_orphan_metabolites(model)
                 for mid in metabolites(model)
-                    @atest mid ∉ orphans "$mid is not an orphan metabolite."
+                    @atest mid ∉ orphans "$mid is not an orphan metabolite"
                 end
             end
             @testset "No deadend metabolites" begin
                 deadends = Metabolites.find_deadend_metabolites(model)
                 for mid in metabolites(model)
-                    @atest mid ∉ deadends "$mid is not a deadend metabolite."
+                    @atest mid ∉ deadends "$mid is not a deadend metabolite"
                 end
             end
             @testset "No disconnected metabolites" begin
                 disconnected = Metabolites.find_disconnected_metabolites(model)
                 for mid in metabolites(model)
-                    @atest mid ∉ disconnected "$mid is not disconnected."
+                    @atest mid ∉ disconnected "$mid is not disconnected"
                 end
             end
         end
@@ -308,13 +318,13 @@ function run_tests(
         @info "Testing the network information..."
         @testset "Network information" begin
             @atest Network.stoichiometric_max_min_ratio(model) <
-                   config.network.condition_number "The stoichiometric matrix is well conditioned."
+                   config.network.condition_number "The stoichiometric matrix is well conditioned"
 
             @testset "No stoichiometrically balanced cycles (reactions)" begin
                 rxns_in_cycles =
                     Network.find_cycle_reactions(model, optimizer; config, workers)
                 for rid in reactions(model)
-                    @atest rid ∉ rxns_in_cycles "$rid does not take part in a stoichiometrically balanced cycle."
+                    @atest rid ∉ rxns_in_cycles "$rid does not take part in a stoichiometrically balanced cycle"
                 end
             end
             @testset "No universally blocked reactions" begin
@@ -325,7 +335,7 @@ function run_tests(
                     workers,
                 )
                 for rid in reactions(model)
-                    @atest rid ∉ blocked_rxns "$rid is not a universally blocked reaction."
+                    @atest rid ∉ blocked_rxns "$rid is not a universally blocked reaction"
                 end
             end
         end
diff --git a/test/data.jl b/test/data.jl
index 6b29375..7618714 100644
--- a/test/data.jl
+++ b/test/data.jl
@@ -44,6 +44,11 @@ model_file = Dict(
             "http://bigg.ucsd.edu/static/models/iML1515.json",
             "b0f9199f048779bb08a14dfa6c09ec56d35b8750d2f99681980d0f098355fbf5",
         ),
+        (
+            "yeast-GEM.xml",
+            "https://raw.githubusercontent.com/SysBioChalmers/yeast-GEM/main/model/yeast-GEM.xml",
+            "c728b09d849b744ec7640cbf15776d40fb2d9cbd0b76a840a8661b626c1bd4be",
+        ),
     ]
 )
 
@@ -51,3 +56,4 @@ model_file = Dict(
 model = load_model(model_file["e_coli_core.json"])
 iJN746 = load_model(model_file["iJN746.json"])
 iML1515 = load_model(StandardModel, model_file["iML1515.json"])
+yeastgem = load_model(StandardModel, model_file["yeast-GEM.xml"])
diff --git a/test/memote.jl b/test/memote.jl
index b67cc44..6b2a2e2 100644
--- a/test/memote.jl
+++ b/test/memote.jl
@@ -21,8 +21,8 @@ using FBCModelTests.Memote.Metabolites
         )
     end
 
-    @test result.passes == 1783
-    @test result.fails == 12
+    @test result.passes == 1857
+    @test result.fails == 33
     @test result.errs == 1 # broken test is the skipped test: model_has_no_erroneous_energy_generating_cycles
 end
 
@@ -60,14 +60,14 @@ end
     @test Annotation.is_annotated_metabolite(model, mid)
     @test Annotation.is_annotated_gene(model, gid)
 
-    @test "ncbiprotein" in Annotation.findall_unannotated_gene_databases(model, gid)
-    @test "inchi" in Annotation.findall_unannotated_metabolite_databases(model, mid)
-    @test "brenda" in Annotation.findall_unannotated_reaction_databases(model, rid)
+    @test "ncbiprotein" ∉ Annotation.findall_annotated_gene_databases(model, gid)
+    @test "inchi" ∉ Annotation.findall_annotated_metabolite_databases(model, mid)
+    @test "brenda" ∉ Annotation.findall_annotated_reaction_databases(model, rid)
 
-    @test "ncbigi" in Annotation.findall_nonconformal_gene_annotations(model, gid)
-    @test "reactome.compound" in
-          Annotation.findall_nonconformal_metabolite_annotations(model, mid)
-    @test isempty(Annotation.findall_nonconformal_reaction_annotations(model, rid))
+    @test "ncbigi" ∉ Annotation.findall_conformal_gene_annotations(model, gid)
+    @test "reactome.compound" ∉
+          Annotation.findall_conformal_metabolite_annotations(model, mid)
+    @test length(Annotation.findall_conformal_reaction_annotations(model, rid)) == 7
 end
 
 @testset "Biomass" begin
@@ -129,9 +129,11 @@ end
 
 @testset "Metabolite" begin
     @test isempty(Metabolites.metabolites_duplicated_in_compartment(model))
-    @test isempty(Metabolites.find_orphan_metabolites(model))
+    @test "mal__L_e" in Metabolites.find_orphan_metabolites(model)
     @test isempty(Metabolites.find_deadend_metabolites(model))
     @test isempty(Metabolites.find_disconnected_metabolites(model))
+    @test length(Metabolites.find_orphan_metabolites(iML1515)) == 65
+    @test length(Metabolites.find_deadend_metabolites(iML1515)) == 63
 
     negative_model = convert(StandardModel, deepcopy(model))
     dup = deepcopy(negative_model.metabolites["atp_c"])