Analyze Contributions of different methods to Annotation

This notebook analyzes relative contributions of different IEA methods to annotation

[1]:

from oaklib import get_adapter
from oaklib.datamodels.vocabulary import IS_A, PART_OF
from oaklib.datamodels.association import Association
from oaklib.parsers.gaf_association_parser import GafAssociationColumns
from oaklib.utilities.associations.association_differ import AssociationDiffer
from oaklib.utilities.subsets.slimmer_utils import filter_redundant
import pandas as pd

# Get a GO handle
go = get_adapter("sqlite:obo:go")

[2]:

# Data Dictionary
GENE = GafAssociationColumns.local_id.value
TERM = GafAssociationColumns.ontology_class_ref.value

[3]:

# Cache HTTP requests
import requests_cache
requests_cache.install_cache("output/requests_cache")

[ ]:

# Alias for GO command line queries

[53]:

%alias go runoak -i sqlite:obo:go

Routine to parse a GAF to a DataFrame

[7]:

def gaf2df(path: str) -> pd.DataFrame:
    df = pd.read_csv(path, sep="\t", comment="!", names=[c.value for c in GafAssociationColumns])
    return df.query(f"'|' not in qualifiers")

df = gaf2df("../../tests/input/mgi-truncated.gaf")
df

[7]:

	db	local_id	db_object_symbol	qualifiers	ontology_class_ref	supporting_references	evidence_type	with_or_from	aspect	db_object_name	db_object_synonyms	db_object_type	db_object_taxon	annotation_date	assigned_by	annotation_extensions	gene_product_form
0	MGI	MGI:1918911	0610005C13Rik	enables	GO:0003674	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	F	RIKEN cDNA 0610005C13 gene	NaN	gene	taxon:10090	20200917	MGI	NaN	NaN
1	MGI	MGI:1918911	0610005C13Rik	is_active_in	GO:0005575	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	C	RIKEN cDNA 0610005C13 gene	NaN	gene	taxon:10090	20100209	MGI	NaN	NaN
2	MGI	MGI:1918911	0610005C13Rik	involved_in	GO:0008150	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	P	RIKEN cDNA 0610005C13 gene	NaN	gene	taxon:10090	20100209	MGI	NaN	NaN
3	MGI	MGI:1923503	0610006L08Rik	enables	GO:0003674	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	F	RIKEN cDNA 0610006L08 gene	NaN	gene	taxon:10090	20120430	MGI	NaN	NaN
4	MGI	MGI:1923503	0610006L08Rik	is_active_in	GO:0005575	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	C	RIKEN cDNA 0610006L08 gene	NaN	gene	taxon:10090	20120430	MGI	NaN	NaN
5	MGI	MGI:1923503	0610006L08Rik	involved_in	GO:0008150	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	P	RIKEN cDNA 0610006L08 gene	NaN	gene	taxon:10090	20120430	MGI	NaN	NaN
6	MGI	MGI:1925547	0610008J02Rik	enables	GO:0003674	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	F	RIKEN cDNA 0610008J02 gene	NaN	gene	taxon:10090	20210426	MGI	NaN	NaN
7	MGI	MGI:1925547	0610008J02Rik	is_active_in	GO:0005575	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	C	RIKEN cDNA 0610008J02 gene	NaN	gene	taxon:10090	20210426	MGI	NaN	NaN
8	MGI	MGI:1925547	0610008J02Rik	involved_in	GO:0008150	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	P	RIKEN cDNA 0610008J02 gene	NaN	gene	taxon:10090	20210426	MGI	NaN	NaN
9	MGI	MGI:1913300	0610009B22Rik	involved_in	GO:0001501	MGI:MGI:4834177\|GO_REF:0000096	ISO	UniProtKB:P0DI81	P	RIKEN cDNA 0610009B22 gene	NaN	protein	taxon:10090	20110927	MGI	NaN	NaN
10	MGI	MGI:1913300	0610009B22Rik	located_in	GO:0005634	MGI:MGI:4834177\|GO_REF:0000096	ISO	UniProtKB:P0DI81	C	RIKEN cDNA 0610009B22 gene	NaN	protein	taxon:10090	20160909	MGI	NaN	NaN
11	MGI	MGI:1913300	0610009B22Rik	located_in	GO:0005654	MGI:MGI:4834177\|GO_REF:0000096	ISO	UniProtKB:P0DI81	C	RIKEN cDNA 0610009B22 gene	NaN	protein	taxon:10090	20151016	MGI	NaN	NaN
12	MGI	MGI:1913300	0610009B22Rik	located_in	GO:0005783	MGI:MGI:4834177\|GO_REF:0000096	ISO	UniProtKB:P0DI81	C	RIKEN cDNA 0610009B22 gene	NaN	protein	taxon:10090	20151016	MGI	NaN	NaN
13	MGI	MGI:1913300	0610009B22Rik	part_of	GO:0030008	MGI:MGI:4834177\|GO_REF:0000096	ISO	UniProtKB:P0DI81	C	RIKEN cDNA 0610009B22 gene	NaN	protein	taxon:10090	20170627	MGI	NaN	NaN
14	MGI	MGI:1913300	0610009B22Rik	located_in	GO:0043231	MGI:MGI:4834177\|GO_REF:0000096	ISO	UniProtKB:P0DI81	C	RIKEN cDNA 0610009B22 gene	NaN	protein	taxon:10090	20151016	MGI	NaN	NaN
15	MGI	MGI:1913300	0610009B22Rik	enables	GO:0044325	MGI:MGI:4834177\|GO_REF:0000096	ISO	UniProtKB:P0DI81	F	RIKEN cDNA 0610009B22 gene	NaN	protein	taxon:10090	20130215	MGI	NaN	NaN
16	MGI	MGI:1913300	0610009B22Rik	located_in	GO:0048471	MGI:MGI:4834177\|GO_REF:0000096	ISO	UniProtKB:P0DI81	C	RIKEN cDNA 0610009B22 gene	NaN	protein	taxon:10090	20130215	MGI	NaN	NaN
17	MGI	MGI:3698435	0610009E02Rik	enables	GO:0003674	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	F	RIKEN cDNA 0610009E02 gene	NaN	gene	taxon:10090	20100209	MGI	NaN	NaN
18	MGI	MGI:3698435	0610009E02Rik	is_active_in	GO:0005575	MGI:MGI:2156816\|GO_REF:0000015	ND	NaN	C	RIKEN cDNA 0610009E02 gene	NaN	gene	taxon:10090	20100209	MGI	NaN	NaN

[14]:

COMMON = "common"
UNIQUE1 = "unique1"
UNIQUE2 = "unique2"

def old_compare_gene_dfs(gene, df1, df2, preds=None):
    terms1 = set(df1[TERM])
    terms2 = set(df2[TERM])
    closure1 = set(list(go.ancestors(list(terms1), preds)))
    closure2 = set(list(go.ancestors(list(terms2), preds)))
    nr_closure1 = set(filter_redundant(go, closure1, preds))
    nr_closure2 = set(filter_redundant(go, closure2, preds))
    unique1 = nr_closure1.difference(nr_closure2)
    unique2 = nr_closure2.difference(nr_closure1)
    return {GENE: gene, UNIQUE1: unique1, UNIQUE2: unique2}

def old_compare_gaf_dfs(df1, df2, preds=[IS_A, PART_OF]):
    genes1 = set(df1[GENE])
    genes2 = set(df2[GENE])
    objs = []
    for gene in genes1.union(genes2):
        subdf1 = df1.query(f"{GENE} == '{gene}'")
        subdf2 = df2.query(f"{GENE} == '{gene}'")
        for obj in compare_gene_dfs(gene, subdf1, subdf2, preds):
            objs.append(obj)
    return pd.DataFrame(objs)

compare_gaf_dfs(df1, df2, preds=[IS_A, PART_OF])

[14]:

	0
0	local_id
1	unique1
2	unique2
3	local_id
4	unique1
5	unique2
6	local_id
7	unique1
8	unique2
9	local_id
10	unique1
11	unique2
12	local_id
13	unique1
14	unique2

Function to analyze contribution

[88]:

def df2assocs(df):
    for _, row in df.iterrows():
        yield Association(subject=row[GENE], object=row[TERM])

def compare_gaf_dfs(df1, df2, preds=[IS_A, PART_OF]):
    """
    Perform an association diff between two GAF DataFrames
    """
    assocs1 = list(df2assocs(df1))
    assocs2 = list(df2assocs(df2))
    differ = AssociationDiffer(go)
    objs = []
    for ch in differ.calculate_change_objects(assocs1, assocs2, preds):
        objs.append(ch)
    return pd.DataFrame(objs).dropna(axis=1, how='all')

compare_gaf_dfs(df1, df2, preds=[IS_A, PART_OF])

[88]:

	publications	subject	old_object	new_object	is_creation	is_deletion	closure_predicates	closure_delta
0	[]	MGI:3698435	None	GO:0003674	True	None	[]	3
1	[]	MGI:3698435	None	GO:0005575	True	None	[]	4
2	[]	MGI:1918911	None	GO:0003674	True	None	[]	3
3	[]	MGI:1918911	None	GO:0005575	True	None	[]	4
4	[]	MGI:1918911	None	GO:0008150	True	None	[]	3
5	[]	MGI:1925547	None	GO:0003674	True	None	[]	3
6	[]	MGI:1925547	None	GO:0005575	True	None	[]	4
7	[]	MGI:1925547	None	GO:0008150	True	None	[]	3
8	[]	MGI:1923503	None	GO:0003674	True	None	[]	3
9	[]	MGI:1923503	None	GO:0005575	True	None	[]	4
10	[]	MGI:1923503	None	GO:0008150	True	None	[]	3
11	[]	MGI:1913300	GO:0001501	None	None	True	[]	-9
12	[]	MGI:1913300	GO:0005634	None	None	True	[]	-19
13	[]	MGI:1913300	GO:0005654	None	None	True	[]	-24
14	[]	MGI:1913300	GO:0005783	None	None	True	[]	-21
15	[]	MGI:1913300	GO:0030008	None	None	True	[]	-9
16	[]	MGI:1913300	GO:0043231	None	None	True	[]	-18
17	[]	MGI:1913300	GO:0044325	None	None	True	[]	-6
18	[]	MGI:1913300	GO:0048471	None	None	True	[]	-16

Human GAF analysis

[89]:

!mkdir -p input

[22]:

!curl -L -s http://release.geneontology.org/2023-04-01/annotations/goa_human.gaf.gz | gzip -dc > input/goa_human.gaf

[28]:

!head input/goa_human.gaf

!gaf-version: 2.2
!
!generated-by: GOC
!
!date-generated: 2023-04-02T12:17
!
!Header from source association file:
!=================================
!
!generated-by: GOC

[29]:

df = gaf2df("input/goa_human.gaf")

/var/folders/nc/m4tx21912kv1b8nk3zzx9plr0000gn/T/ipykernel_40496/2095927277.py:2: DtypeWarning: Columns (15) have mixed types. Specify dtype option on import or set low_memory=False.
  df = pd.read_csv(path, sep="\t", comment="!", names=[c.value for c in GafAssociationColumns])

[30]:

df

[30]:

	db	local_id	db_object_symbol	qualifiers	ontology_class_ref	supporting_references	evidence_type	with_or_from	aspect	db_object_name	db_object_synonyms	db_object_type	db_object_taxon	annotation_date	assigned_by	annotation_extensions	gene_product_form
0	UniProtKB	A0A024RBG1	NUDT4B	enables	GO:0003723	GO_REF:0000043	IEA	UniProtKB-KW:KW-0694	F	Diphosphoinositol polyphosphate phosphohydrola...	NUDT4B	protein	taxon:9606	20230306	UniProt	NaN	NaN
1	UniProtKB	A0A024RBG1	NUDT4B	enables	GO:0046872	GO_REF:0000043	IEA	UniProtKB-KW:KW-0479	F	Diphosphoinositol polyphosphate phosphohydrola...	NUDT4B	protein	taxon:9606	20230306	UniProt	NaN	NaN
2	UniProtKB	A0A024RBG1	NUDT4B	located_in	GO:0005829	GO_REF:0000052	IDA	NaN	C	Diphosphoinositol polyphosphate phosphohydrola...	NUDT4B	protein	taxon:9606	20161204	HPA	NaN	NaN
3	UniProtKB	A0A075B6H7	IGKV3-7	involved_in	GO:0002250	GO_REF:0000043	IEA	UniProtKB-KW:KW-1064	P	Probable non-functional immunoglobulin kappa v...	IGKV3-7	protein	taxon:9606	20230306	UniProt	NaN	NaN
4	UniProtKB	A0A075B6H7	IGKV3-7	located_in	GO:0005886	GO_REF:0000044	IEA	UniProtKB-SubCell:SL-0039	C	Probable non-functional immunoglobulin kappa v...	IGKV3-7	protein	taxon:9606	20230306	UniProt	NaN	NaN
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
630736	UniProtKB	P35580	MYH10	involved_in	GO:0031032	PMID:21873635	IBA	PANTHER:PTN002897265\|UniProtKB:P35580\|MGI:MGI:...	P	Myosin-10	MYH10	protein	taxon:9606	20220223	GO_Central	NaN	NaN
630737	UniProtKB	Q10472	GALNT1	involved_in	GO:0006493	PMID:21873635	IBA	PANTHER:PTN004287905\|WB:WBGene00001630\|UniProt...	P	Polypeptide N-acetylgalactosaminyltransferase 1	GALNT1	protein	taxon:9606	20230110	GO_Central	NaN	NaN
630738	UniProtKB	Q6NXT2	H3-5	is_active_in	GO:0005634	PMID:21873635	IBA	PANTHER:PTN008517671\|dictyBase:DDB_G0271092\|Un...	C	Histone H3.3C	H3-5\|H3F3C	protein	taxon:9606	20230110	GO_Central	NaN	NaN
630739	UniProtKB	Q9NS87	KIF15	is_active_in	GO:0005874	PMID:21873635	IBA	PANTHER:PTN000648413\|UniProtKB:C8V3Q8\|UniProtK...	C	Kinesin-like protein KIF15	KIF15\|KLP2\|KNSL7	protein	taxon:9606	20230111	GO_Central	NaN	NaN
630740	UniProtKB	P01889	HLA-B	is_active_in	GO:0005615	PMID:21873635	IBA	PANTHER:PTN002703355\|UniProtKB:Q30201\|UniProtK...	C	HLA class I histocompatibility antigen, B alph...	HLA-B\|HLAB	protein	taxon:9606	20181121	GO_Central	NaN	NaN

630741 rows × 17 columns

[38]:

iea = df.query("evidence_type == 'IEA'")
iea.groupby(['supporting_references']).count()

[38]:

	db	local_id	db_object_symbol	qualifiers	ontology_class_ref	evidence_type	with_or_from	aspect	db_object_name	db_object_synonyms	db_object_type	db_object_taxon	annotation_date	assigned_by	annotation_extensions	gene_product_form
supporting_references
GO_REF:0000002	6331	6331	6331	6331	6331	6331	6331	6331	6331	6321	6331	6331	6331	6331	0	0
GO_REF:0000003	1052	1052	1052	1052	1052	1052	1052	1052	1052	1052	1052	1052	1052	1052	0	0
GO_REF:0000041	738	738	738	738	738	738	738	738	738	738	738	738	738	738	0	0
GO_REF:0000043	13433	13433	13433	13433	13433	13433	13433	13433	13433	13418	13433	13433	13433	13433	0	0
GO_REF:0000044	8086	8086	8086	8086	8086	8086	8086	8086	8086	8073	8086	8086	8086	8086	0	0
GO_REF:0000104	199	199	199	199	199	199	199	199	199	199	199	199	199	199	0	0
GO_REF:0000107	39108	39108	39108	39108	39108	39108	39108	39108	39108	39108	39108	39108	39108	39108	0	0
GO_REF:0000108	3680	3680	3680	3680	3680	3680	3680	3680	3680	3678	3680	3680	3680	3680	0	0
GO_REF:0000116	1147	1147	1147	1147	1147	1147	1147	1147	1147	1147	1147	1147	1147	1147	0	0
GO_REF:0000117	214	214	214	214	214	214	214	214	214	213	214	214	214	214	0	0

Fetch all GOREFs

[39]:

gorefs = set(iea['supporting_references'])
gorefs

[39]:

{'GO_REF:0000002',
 'GO_REF:0000003',
 'GO_REF:0000041',
 'GO_REF:0000043',
 'GO_REF:0000044',
 'GO_REF:0000104',
 'GO_REF:0000107',
 'GO_REF:0000108',
 'GO_REF:0000116',
 'GO_REF:0000117'}

[65]:

def add_labels(df):
    """
    Annotate Diff DataFrame with labels for the objects that are "lost"
    """
    df["old_object_label"] = df.apply(lambda row: go.label(row["old_object"]), axis=1)

[42]:

def analyze_iea(df, ref):
    """
    Simulate deleting the IEAs with the stated reference.
    """
    df_minus = df.query(f'supporting_references != "{ref}"')
    return compare_gaf_dfs(df, df_minus)

[42]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta
0	[]	P22612	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1
1	[]	Q9Y3S1	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1
2	[]	Q9NUU7	GO:0016887	False	True	[rdfs:subClassOf, BFO:0000050]	-6
3	[]	Q16584	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1
4	[]	P17516	GO:0047045	False	True	[rdfs:subClassOf, BFO:0000050]	-1
...	...	...	...	...	...	...	...
720	[]	Q5VST9	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1
721	[]	O43293	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1
722	[]	Q9H2U1	GO:0016887	False	True	[rdfs:subClassOf, BFO:0000050]	-6
723	[]	Q6DHV7	GO:0062154	False	True	[rdfs:subClassOf, BFO:0000050]	-1
724	[]	Q5TCX8	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1

725 rows × 7 columns

RHEA

[43]:

rhea = analyze_iea(df, "GO_REF:0000116")

[66]:

add_labels(rhea)
rhea

[66]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	old_object_label
0	[]	P22612	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1	protein serine kinase activity
1	[]	Q9Y3S1	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1	protein serine kinase activity
2	[]	Q9NUU7	GO:0016887	False	True	[rdfs:subClassOf, BFO:0000050]	-6	ATP hydrolysis activity
3	[]	Q16584	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1	protein serine kinase activity
4	[]	P17516	GO:0047045	False	True	[rdfs:subClassOf, BFO:0000050]	-1	testosterone 17-beta-dehydrogenase (NADP+) act...
...	...	...	...	...	...	...	...	...
720	[]	Q5VST9	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1	protein serine kinase activity
721	[]	O43293	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1	protein serine kinase activity
722	[]	Q9H2U1	GO:0016887	False	True	[rdfs:subClassOf, BFO:0000050]	-6	ATP hydrolysis activity
723	[]	Q6DHV7	GO:0062154	False	True	[rdfs:subClassOf, BFO:0000050]	-1	N6-methyl-AMP deaminase activity
724	[]	Q5TCX8	GO:0106310	False	True	[rdfs:subClassOf, BFO:0000050]	-1	protein serine kinase activity

725 rows × 8 columns

[70]:

lbl = ['old_object', 'old_object_label']
rhea.groupby(lbl).mean(numeric_only=True)

[70]:

		old_object_obsolete	is_deletion	closure_delta
old_object	old_object_label
GO:0002083	4-hydroxybenzoate decaprenyltransferase activity	0.0	1.0	-2.0
GO:0003924	GTPase activity	0.0	1.0	-5.0
GO:0003954	NADH dehydrogenase activity	0.0	1.0	-1.0
GO:0004052	arachidonate 12(S)-lipoxygenase activity	0.0	1.0	-1.0
GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	0.0	1.0	-2.0
...	...	...	...	...
GO:0140947	histone H3K9me2 methyltransferase activity	0.0	1.0	-1.0
GO:0140948	histone H3K9 monomethyltransferase activity	0.0	1.0	-1.0
GO:1901480	oleate transmembrane transporter activity	0.0	1.0	-1.0
GO:1990002	methylglyoxal reductase (NADPH-dependent, acetol producing)	0.0	1.0	-1.0
GO:1990362	butanol dehydrogenase activity	0.0	1.0	-1.0

153 rows × 3 columns

[73]:

pd.set_option('display.max_rows', 1000)
rhea.groupby(lbl).min(numeric_only=True).sort_values("closure_delta")

[73]:

		old_object_obsolete	is_deletion	closure_delta
old_object	old_object_label
GO:0016279	protein-lysine N-methyltransferase activity	False	True	-10
GO:0140933	5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity	False	True	-9
GO:0016887	ATP hydrolysis activity	False	True	-7
GO:0003924	GTPase activity	False	True	-7
GO:0052665	tRNA (uracil-2'-O-)-methyltransferase activity	False	True	-4
GO:0036134	12-hydroxyheptadecatrienoic acid synthase activity	False	True	-4
GO:0004713	protein tyrosine kinase activity	False	True	-4
GO:0090555	phosphatidylethanolamine flippase activity	False	True	-4
GO:0097023	fructose 6-phosphate aldolase activity	False	True	-4
GO:0004165	delta(3)-delta(2)-enoyl-CoA isomerase activity	False	True	-4
GO:0106294	NADPH oxidase H202-forming activity	False	True	-4
GO:0090556	phosphatidylserine floppase activity	False	True	-3
GO:0047748	cholestanetetraol 26-dehydrogenase activity	False	True	-3
GO:0016290	palmitoyl-CoA hydrolase activity	False	True	-3
GO:0004722	protein serine/threonine phosphatase activity	False	True	-3
GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	False	True	-3
GO:0140567	membrane protein dislocase activity	False	True	-3
GO:0047045	testosterone 17-beta-dehydrogenase (NADP+) activity	False	True	-3
GO:0008458	carnitine O-octanoyltransferase activity	False	True	-3
GO:0102391	decanoate-CoA ligase activity	False	True	-2
GO:0047956	glycerol dehydrogenase [NADP+] activity	False	True	-2
GO:0062189	anandamide 14,15 epoxidase activity	False	True	-2
GO:0043262	ADP phosphatase activity	False	True	-2
GO:0106347	U2 snRNA 2'-O-methyladenosine m6 methyltransferase activity	False	True	-2
GO:0042054	histone methyltransferase activity	False	True	-2
GO:0034485	phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity	False	True	-2
GO:0047451	(3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity	False	True	-2
GO:0043759	methylbutanoate-CoA ligase activity	False	True	-2
GO:0106156	peptidyl-lysine 4-dioxygenase activity	False	True	-2
GO:0044594	17-beta-hydroxysteroid dehydrogenase (NAD+) activity	False	True	-2
GO:0047376	all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity	False	True	-2
GO:0106364	4-hydroxy-3-all-trans-hexaprenylbenzoate oxygenase activity	False	True	-2
GO:0034480	phosphatidylcholine phospholipase C activity	False	True	-2
GO:0002083	4-hydroxybenzoate decaprenyltransferase activity	False	True	-2
GO:0047035	testosterone dehydrogenase (NAD+) activity	False	True	-2
GO:0062188	anandamide 11,12 epoxidase activity	False	True	-2
GO:0062187	anandamide 8,9 epoxidase activity	False	True	-2
GO:0090554	phosphatidylcholine floppase activity	False	True	-2
GO:0004317	(3R)-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity	False	True	-2
GO:0051922	cholesterol sulfotransferase activity	False	True	-2
GO:0004439	phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity	False	True	-2
GO:0016312	inositol bisphosphate phosphatase activity	False	True	-2
GO:0052848	inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity	False	True	-2
GO:0015417	ABC-type polyamine transporter activity	False	True	-2
GO:0008106	alcohol dehydrogenase (NADP+) activity	False	True	-2
GO:0052845	inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity	False	True	-2
GO:0008970	phospholipase A1 activity	False	True	-2
GO:0019705	protein-cysteine S-myristoyltransferase activity	False	True	-2
GO:0008693	(3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity	False	True	-2
GO:0106009	(4S)-4-hydroxy-2-oxoglutarate aldolase activity	False	True	-1
GO:0102336	3-oxo-arachidoyl-CoA synthase activity	False	True	-1
GO:0103026	fructose-1-phosphatase activity	False	True	-1
GO:0098606	selenocystathionine gamma-lyase activity	False	True	-1
GO:0102991	myristoyl-CoA hydrolase activity	False	True	-1
GO:0102662	malonate-semialdehyde dehydrogenase (acetylating, NAD+) activity	False	True	-1
GO:0102354	11-cis-retinol dehydrogenase activity	False	True	-1
GO:0102149	farnesylcysteine lyase activity	False	True	-1
GO:0102175	3-beta-hydroxysteroid dehydrogenase/C4-decarboxylase activity	False	True	-1
GO:0102338	3-oxo-lignoceronyl-CoA synthase activity	False	True	-1
GO:0102337	3-oxo-cerotoyl-CoA synthase activity	False	True	-1
GO:0106008	2-oxoglutaramate amidase activity	False	True	-1
GO:0097383	dIDP phosphatase activity	False	True	-1
GO:0106375	deoxynucleoside triphosphate hydrolase activity	False	True	-1
GO:0106237	arachidonate 12(R)-lipoxygenase activity	False	True	-1
GO:1901480	oleate transmembrane transporter activity	False	True	-1
GO:0140948	histone H3K9 monomethyltransferase activity	False	True	-1
GO:0140947	histone H3K9me2 methyltransferase activity	False	True	-1
GO:0140945	histone H3K4 monomethyltransferase activity	False	True	-1
GO:0140944	histone H4K20 monomethyltransferase activity	False	True	-1
GO:0140943	histone H4K20 trimethyltransferase activity	False	True	-1
GO:0140941	histone H4K20me methyltransferase activity	False	True	-1
GO:0140818	mRNA 5'-phosphatase activity	False	True	-1
GO:0140804	NAD+- protein-lysine ADP-ribosyltransferase activity	False	True	-1
GO:0140803	NAD+- protein-cysteine ADP-ribosyltransferase activity	False	True	-1
GO:0140683	histone H3K9me/H3K9me2 demethylase activity	False	True	-1
GO:0140562	EGF-domain serine xylosyltransferase activity	False	True	-1
GO:0140561	EGF-domain serine glucosyltransferase activity	False	True	-1
GO:0106226	peptide 2-hydroxyisobutyryltransferase activity	False	True	-1
GO:0140439	protein-cysteine S-stearoyltransferase activity	False	True	-1
GO:0120243	2-iminopropanoate deaminase activity	False	True	-1
GO:0120092	crotonyl-CoA hydratase activity	False	True	-1
GO:0110153	RNA NAD-cap (NMN-forming) hydrolase activity	False	True	-1
GO:0106433	O6-methyl-dGTP hydrolase activity	False	True	-1
GO:0106431	N6-methyl-(d)ATP hydrolase activity	False	True	-1
GO:0106399	acyl-coenzyme A diphosphatase activity	False	True	-1
GO:0106386	(3R)-hydroxyacyl-CoA dehydrogenase (NAD) activity	False	True	-1
GO:0106376	2-hydroxyphytanoyl-CoA lyase activity	False	True	-1
GO:0106329	L-phenylalaine oxidase activity	False	True	-1
GO:0106313	methylenetetrahydrofolate reductase NADPH activity	False	True	-1
GO:0106310	protein serine kinase activity	False	True	-1
GO:0106301	arachidonic acid 5,6-epoxygenase activity	False	True	-1
GO:0106293	NADH oxidase H202-forming activity	False	True	-1
GO:0120298	peptide noradrenalinyltransferase activity	False	True	-1
GO:0080079	cellobiose glucosidase activity	False	True	-1
GO:0047982	homocysteine desulfhydrase activity	False	True	-1
GO:0070251	pristanate-CoA ligase activity	False	True	-1
GO:0036220	ITP diphosphatase activity	False	True	-1
GO:0036219	GTP diphosphatase activity	False	True	-1
GO:0036218	dTTP diphosphatase activity	False	True	-1
GO:0036130	prostaglandin H2 endoperoxidase reductase activity	False	True	-1
GO:0035870	dITP diphosphatase activity	False	True	-1
GO:0035242	protein-arginine omega-N asymmetric methyltransferase activity	False	True	-1
GO:0035241	protein-arginine omega-N monomethyltransferase activity	False	True	-1
GO:0033779	5beta-cholestane-3alpha,7alpha-diol 12alpha-hydroxylase activity	False	True	-1
GO:0033703	3beta-hydroxy-5beta-steroid dehydrogenase activity	False	True	-1
GO:0031956	medium-chain fatty acid-CoA ligase activity	False	True	-1
GO:0018820	cyanamide hydratase activity	False	True	-1
GO:0016617	4-oxoproline reductase activity	False	True	-1
GO:0010308	acireductone dioxygenase (Ni2+-requiring) activity	False	True	-1
GO:0008983	protein-glutamate O-methyltransferase activity	False	True	-1
GO:0008753	NADPH dehydrogenase (quinone) activity	False	True	-1
GO:0008405	arachidonic acid 11,12-epoxygenase activity	False	True	-1
GO:0008404	arachidonic acid 14,15-epoxygenase activity	False	True	-1
GO:0004806	triglyceride lipase activity	False	True	-1
GO:0004745	NAD-retinol dehydrogenase activity	False	True	-1
GO:0004427	inorganic diphosphate phosphatase activity	False	True	-1
GO:0004354	glutamate dehydrogenase (NADP+) activity	False	True	-1
GO:0004336	galactosylceramidase activity	False	True	-1
GO:0004180	carboxypeptidase activity	False	True	-1
GO:0004052	arachidonate 12(S)-lipoxygenase activity	False	True	-1
GO:0003954	NADH dehydrogenase activity	False	True	-1
GO:0036221	UTP diphosphatase activity	False	True	-1
GO:0072582	17-beta-hydroxysteroid dehydrogenase (NADP+) activity	False	True	-1
GO:0036222	XTP diphosphatase activity	False	True	-1
GO:0036430	CMP kinase activity	False	True	-1
GO:0062184	testosterone 16-beta-hydroxylase activity	False	True	-1
GO:0062183	all-trans retinoic acid 18-hydroxylase activity	False	True	-1
GO:0062182	all-trans retinoic acid 4-hydrolase activity	False	True	-1
GO:0062154	N6-methyl-AMP deaminase activity	False	True	-1
GO:0052596	phenethylamine:oxygen oxidoreductase (deaminating) activity	False	True	-1
GO:0052595	aliphatic amine oxidase activity	False	True	-1
GO:0050213	progesterone 5-alpha-reductase activity	False	True	-1
GO:0050048	L-leucine:2-oxoglutarate aminotransferase activity	False	True	-1
GO:0047995	hydroxyphenylpyruvate reductase activity	False	True	-1
GO:1990002	methylglyoxal reductase (NADPH-dependent, acetol producing)	False	True	-1
GO:0047975	guanosine phosphorylase activity	False	True	-1
GO:0047935	glucose 1-dehydrogenase (NADP+) activity	False	True	-1
GO:0036403	arachidonate 8(S)-lipoxygenase activity	False	True	-1
GO:0047934	glucose 1-dehydrogenase (NAD+) activity	False	True	-1
GO:0047844	deoxycytidine deaminase activity	False	True	-1
GO:0047693	ATP diphosphatase activity	False	True	-1
GO:0047638	albendazole monooxygenase activity	False	True	-1
GO:0047555	3',5'-cyclic-GMP phosphodiesterase activity	False	True	-1
GO:0047378	acetylalkylglycerol acetylhydrolase activity	False	True	-1
GO:0047022	7-beta-hydroxysteroid dehydrogenase (NADP+) activity	False	True	-1
GO:0046899	nucleoside triphosphate adenylate kinase activity	False	True	-1
GO:0043956	3-hydroxypropionyl-CoA dehydratase activity	False	True	-1
GO:0043878	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity	False	True	-1
GO:0043273	CTPase activity	False	True	-1
GO:0036431	dCMP kinase activity	False	True	-1
GO:0047931	glucosamine kinase activity	False	True	-1
GO:1990362	butanol dehydrogenase activity	False	True	-1
GO:0016937	short-chain-acyl-CoA dehydrogenase activity	False	True	0

[79]:

rhea.groupby("subject").count().query("publications > 3")

[79]:

	publications	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	old_object_label
subject
P22413	4	4	4	4	4	4	4

[80]:

rhea.query("subject == 'P22413'")

[80]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	old_object_label
483	[]	P22413	GO:0036221	False	True	[rdfs:subClassOf, BFO:0000050]	-1	UTP diphosphatase activity
484	[]	P22413	GO:0004115	False	True	[rdfs:subClassOf, BFO:0000050]	-3	3',5'-cyclic-AMP phosphodiesterase activity
485	[]	P22413	GO:0036219	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GTP diphosphatase activity
486	[]	P22413	GO:0047693	False	True	[rdfs:subClassOf, BFO:0000050]	-1	ATP diphosphatase activity

[81]:

rhea[["closure_delta"]].sum()

[81]:

closure_delta   -1341
dtype: int64

ARBA

[74]:

arba = analyze_iea(df, "GO_REF:0000117")

[84]:

add_labels(arba)

[85]:

pd.set_option('display.max_rows', 10)
arba

[85]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	old_object_label
0	[]	Q96JM4	GO:0009966	None	True	[]	-10	regulation of signal transduction
1	[]	Q96MZ0	GO:0005737	None	True	[]	-15	cytoplasm
2	[]	P37275	GO:0044271	False	True	[rdfs:subClassOf, BFO:0000050]	0	cellular nitrogen compound biosynthetic process
3	[]	Q8TC17	GO:0005737	False	True	[rdfs:subClassOf, BFO:0000050]	-15	cytoplasm
4	[]	Q9Y5H1	GO:0007399	False	True	[rdfs:subClassOf, BFO:0000050]	-6	nervous system development
...	...	...	...	...	...	...	...	...
207	[]	P32745	GO:0007187	False	True	[rdfs:subClassOf, BFO:0000050]	-1	G protein-coupled receptor signaling pathway, ...
208	[]	P32745	GO:0008285	False	True	[rdfs:subClassOf, BFO:0000050]	-4	negative regulation of cell population prolife...
209	[]	P29144	GO:0006508	False	True	[rdfs:subClassOf, BFO:0000050]	-1	proteolysis
210	[]	Q9Y5G2	GO:0007399	False	True	[rdfs:subClassOf, BFO:0000050]	-6	nervous system development
211	[]	Q5TH69	GO:0005794	False	True	[rdfs:subClassOf, BFO:0000050]	-1	Golgi apparatus

212 rows × 8 columns

[82]:

arba[["closure_delta"]].sum()

[82]:

closure_delta   -1252
dtype: int64

[86]:

pd.set_option('display.max_rows', 1000)
arba.groupby(lbl).min(numeric_only=True).sort_values("closure_delta")

[86]:

		is_deletion	closure_delta
old_object	old_object_label
GO:0045892	negative regulation of DNA-templated transcription	True	-31
GO:0022625	cytosolic large ribosomal subunit	True	-28
GO:0005783	endoplasmic reticulum	True	-21
GO:0005634	nucleus	True	-19
GO:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	True	-18
GO:0007080	mitotic metaphase plate congression	True	-18
GO:0006470	protein dephosphorylation	True	-16
GO:1901673	regulation of mitotic spindle assembly	True	-16
GO:0005737	cytoplasm	True	-15
GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	True	-14
GO:0006468	protein phosphorylation	True	-14
GO:0005794	Golgi apparatus	True	-14
GO:0016070	RNA metabolic process	True	-14
GO:0046488	phosphatidylinositol metabolic process	True	-14
GO:0001527	microfibril	True	-13
GO:0015012	heparan sulfate proteoglycan biosynthetic process	True	-13
GO:0005828	kinetochore microtubule	True	-12
GO:0046761	viral budding from plasma membrane	True	-12
GO:0098590	plasma membrane region	True	-11
GO:0097352	autophagosome maturation	True	-11
GO:0016925	protein sumoylation	True	-11
GO:0061952	midbody abscission	True	-11
GO:0009966	regulation of signal transduction	True	-10
GO:0005886	plasma membrane	True	-10
GO:0015229	L-ascorbic acid transmembrane transporter activity	True	-10
GO:0031468	nuclear membrane reassembly	True	-9
GO:0043229	intracellular organelle	True	-9
GO:0000776	kinetochore	True	-9
GO:0005930	axoneme	True	-9
GO:0005125	cytokine activity	True	-9
GO:0016020	membrane	True	-8
GO:0006508	proteolysis	True	-8
GO:0016567	protein ubiquitination	True	-7
GO:0001778	plasma membrane repair	True	-7
GO:0110165	cellular anatomical entity	True	-7
GO:0007605	sensory perception of sound	True	-7
GO:0008194	UDP-glycosyltransferase activity	True	-7
GO:0060548	negative regulation of cell death	True	-7
GO:0043565	sequence-specific DNA binding	True	-6
GO:0005643	nuclear pore	True	-6
GO:0006281	DNA repair	True	-6
GO:0016311	dephosphorylation	True	-6
GO:1904930	amphisome membrane	True	-6
GO:0005765	lysosomal membrane	True	-6
GO:0097729	9+2 motile cilium	True	-6
GO:0007399	nervous system development	True	-6
GO:0009925	basal plasma membrane	True	-5
GO:0039702	viral budding via host ESCRT complex	True	-5
GO:0033554	cellular response to stress	True	-5
GO:0033036	macromolecule localization	True	-5
GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	True	-5
GO:0046470	phosphatidylcholine metabolic process	True	-5
GO:0005654	nucleoplasm	True	-5
GO:0007606	sensory perception of chemical stimulus	True	-5
GO:0048468	cell development	True	-5
GO:0015250	water channel activity	True	-4
GO:0008201	heparin binding	True	-4
GO:0051128	regulation of cellular component organization	True	-4
GO:0008285	negative regulation of cell population proliferation	True	-4
GO:0005635	nuclear envelope	True	-4
GO:0005789	endoplasmic reticulum membrane	True	-4
GO:0048583	regulation of response to stimulus	True	-4
GO:0031982	vesicle	True	-3
GO:0071704	organic substance metabolic process	True	-3
GO:0005764	lysosome	True	-2
GO:0061459	L-arginine transmembrane transporter activity	True	-2
GO:0097381	photoreceptor disc membrane	True	-2
GO:0032585	multivesicular body membrane	True	-2
GO:0006950	response to stress	True	-2
GO:0032991	protein-containing complex	True	-2
GO:0005829	cytosol	True	-2
GO:0031640	killing of cells of another organism	True	-2
GO:0031625	ubiquitin protein ligase binding	True	-2
GO:1902774	late endosome to lysosome transport	True	-2
GO:0042802	identical protein binding	True	-2
GO:0008284	positive regulation of cell population proliferation	True	-1
GO:0071705	nitrogen compound transport	True	-1
GO:0071702	organic substance transport	True	-1
GO:0019899	enzyme binding	True	-1
GO:0005576	extracellular region	True	-1
GO:0030496	midbody	True	-1
GO:0031996	thioesterase binding	True	-1
GO:0007187	G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	True	-1
GO:0016570	histone modification	True	-1
GO:0007268	chemical synaptic transmission	True	0
GO:0044271	cellular nitrogen compound biosynthetic process	True	0
GO:0070098	chemokine-mediated signaling pathway	True	0
GO:0071805	potassium ion transmembrane transport	True	0
GO:0006351	DNA-templated transcription	True	0
GO:0007155	cell adhesion	True	0
GO:0006915	apoptotic process	True	0
GO:0007186	G protein-coupled receptor signaling pathway	True	0

All IEAs

[87]:

# this takes some time....
dfs_by_ref = {}
for goref in gorefs:
    print(goref)
    dfs_by_ref[goref] = analyze_iea(df, goref)

[92]:

for k, df in dfs_by_ref.items():
    df["method"] = k

[93]:

dfs_by_ref["GO_REF:0000041"]

[93]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	method
0	[]	Q53EU6	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
1	[]	Q5VZY2	GO:0006644	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
2	[]	P10632	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041
3	[]	Q9NXB9	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
4	[]	Q969V5	GO:0016925	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
5	[]	Q9P2W7	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
6	[]	A6NK59	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
7	[]	Q9H1B5	GO:0030206	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
8	[]	Q693B1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
9	[]	O60927	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
10	[]	Q8WV16	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
11	[]	Q9UK23	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041
12	[]	Q9HAY6	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
13	[]	P30038	GO:0010133	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
14	[]	P20815	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
15	[]	P11172	GO:0044205	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
16	[]	Q9H920	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
17	[]	Q8N9I9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
18	[]	Q8TD30	GO:0042853	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
19	[]	P43304	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041
20	[]	Q8WXH6	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
21	[]	Q9NQC1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
22	[]	Q15370	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
23	[]	P22557	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
24	[]	P08243	GO:0070981	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
25	[]	P36957	GO:0033512	False	True	[rdfs:subClassOf, BFO:0000050]	-21	GO_REF:0000041
26	[]	P13716	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
27	[]	P47895	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041
28	[]	Q9NWM0	GO:0046208	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
29	[]	Q8N7A1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
30	[]	Q4G0X4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
31	[]	P33908	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
32	[]	Q8WXK1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
33	[]	O00635	GO:0016925	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
34	[]	Q9UI17	GO:0006579	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
35	[]	Q9BQ90	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
36	[]	P48448	GO:0006068	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
37	[]	Q12834	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
38	[]	Q13011	GO:0006635	False	True	[rdfs:subClassOf, BFO:0000050]	-28	GO_REF:0000041
39	[]	P08397	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
40	[]	P30566	GO:0006189	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
41	[]	Q96NS5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
42	[]	A6NNE9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
43	[]	Q8NEB5	GO:0006644	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
44	[]	P06132	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
45	[]	P32189	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
46	[]	Q86XS8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
47	[]	Q9BSK4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
48	[]	P00352	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
49	[]	Q9Y315	GO:0046386	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
50	[]	P04181	GO:0055129	False	True	[rdfs:subClassOf, BFO:0000050]	-16	GO_REF:0000041
51	[]	Q6UWP2	GO:0006703	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
52	[]	P24462	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
53	[]	Q92781	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
54	[]	Q15751	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041
55	[]	Q9NRJ4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
56	[]	Q92624	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
57	[]	Q9BY49	GO:0006633	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041
58	[]	Q96M94	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
59	[]	Q96N76	GO:0019556	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
60	[]	Q96N76	GO:0019557	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
61	[]	Q6UWP7	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
62	[]	Q9NXF7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
63	[]	Q9BR09	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
64	[]	Q8NBN7	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000041
65	[]	Q6GTS8	GO:0006631	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
66	[]	Q9H1B7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
67	[]	Q5VVX9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
68	[]	P55263	GO:0044209	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
69	[]	Q9NP56	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
70	[]	P20132	GO:0006094	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
71	[]	Q02127	GO:0044205	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041
72	[]	Q5QP82	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
73	[]	Q99943	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
74	[]	Q9Y4D8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
75	[]	Q16394	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
76	[]	Q7L273	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
77	[]	P49189	GO:0045329	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
78	[]	P11086	GO:0042418	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
79	[]	Q9UKT4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
80	[]	P50416	GO:0006635	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041
81	[]	P0C0E4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
82	[]	P13196	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
83	[]	Q8N5D6	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
84	[]	Q8IUQ4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
85	[]	Q9BUZ4	GO:0043161	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
86	[]	Q8TCG5	GO:0006635	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041
87	[]	Q99618	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
88	[]	Q9NSE2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
89	[]	Q9BXS1	GO:0050992	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
90	[]	P14324	GO:0033384	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
91	[]	Q9GZR1	GO:0016925	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
92	[]	Q6TDP4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
93	[]	Q99685	GO:0019433	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
94	[]	O15524	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
95	[]	Q8TEB1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
96	[]	O60909	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-17	GO_REF:0000041
97	[]	O76074	GO:0046069	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
98	[]	P21673	GO:0009447	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
99	[]	O15120	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
100	[]	Q9NWW6	GO:0009435	False	True	[rdfs:subClassOf, BFO:0000050]	-18	GO_REF:0000041
101	[]	Q8TBB1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
102	[]	Q8WYK0	GO:0006631	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
103	[]	Q9H672	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
104	[]	O95749	GO:0033384	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
105	[]	O95749	GO:0033386	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
106	[]	O95749	GO:0045337	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
107	[]	Q8TB52	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
108	[]	Q9Y4B6	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
109	[]	P04424	GO:0000050	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
110	[]	P23109	GO:0032264	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
111	[]	Q9Y575	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
112	[]	Q5H9S7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
113	[]	O95803	GO:0030210	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
114	[]	P49675	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
115	[]	Q9NRF8	GO:0044210	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
116	[]	Q8NCN4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
117	[]	Q01432	GO:0032264	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
118	[]	Q86XP0	GO:0006631	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
119	[]	Q96EH8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
120	[]	Q06203	GO:0006189	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
121	[]	Q16831	GO:0044206	False	True	[rdfs:subClassOf, BFO:0000050]	-29	GO_REF:0000041
122	[]	Q16719	GO:0097053	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
123	[]	Q9H0C5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
124	[]	O14508	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
125	[]	Q6YFQ2	GO:0006119	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
126	[]	Q8TBF5	GO:0006506	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
127	[]	Q13907	GO:0050992	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
128	[]	Q02928	GO:0031408	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
129	[]	Q8TEB7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
130	[]	P05089	GO:0000050	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
131	[]	Q8N5Z0	GO:0033512	False	True	[rdfs:subClassOf, BFO:0000050]	-40	GO_REF:0000041
132	[]	Q8NHY2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
133	[]	P49641	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
134	[]	P10746	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
135	[]	A8MWK0	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-20	GO_REF:0000041
136	[]	Q9H2A2	GO:0097053	False	True	[rdfs:subClassOf, BFO:0000050]	-23	GO_REF:0000041
137	[]	Q8WXH5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
138	[]	O43255	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
139	[]	Q9NRZ7	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
140	[]	Q5XUX0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
141	[]	Q9UKM7	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
142	[]	P37058	GO:0061370	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
143	[]	O00763	GO:2001295	False	True	[rdfs:subClassOf, BFO:0000050]	-24	GO_REF:0000041
144	[]	Q5T197	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
145	[]	O14543	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
146	[]	Q14409	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
147	[]	Q9HBH5	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000041
148	[]	Q16706	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
149	[]	P52849	GO:0030210	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
150	[]	O14732	GO:0006021	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
151	[]	Q9H477	GO:0019303	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
152	[]	Q12882	GO:0019483	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041
153	[]	Q5XPI4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
154	[]	Q96NU7	GO:0019556	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
155	[]	Q96NU7	GO:0019557	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
156	[]	P78540	GO:0000050	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
157	[]	Q96S21	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
158	[]	P22570	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
159	[]	Q8IY47	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
160	[]	O60513	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
161	[]	Q6P050	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
162	[]	Q86WB0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
163	[]	Q13946	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
164	[]	Q9UDR5	GO:0033512	False	True	[rdfs:subClassOf, BFO:0000050]	-25	GO_REF:0000041
165	[]	Q01433	GO:0032264	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
166	[]	Q9H3R1	GO:0030210	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
167	[]	Q08499	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
168	[]	Q9UK99	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
169	[]	P50336	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
170	[]	Q9NXK8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
171	[]	Q9NV06	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
172	[]	Q5T6F0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
173	[]	Q9NPZ5	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
174	[]	Q6ZS86	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
175	[]	Q8IWU9	GO:0042427	False	True	[rdfs:subClassOf, BFO:0000050]	-21	GO_REF:0000041
176	[]	Q14410	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
177	[]	P04818	GO:0006235	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
178	[]	Q8IWR1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
179	[]	O60512	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
180	[]	P42357	GO:0019556	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
181	[]	P42357	GO:0019557	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
182	[]	Q9NRD1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
183	[]	Q9NYL5	GO:0006707	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
184	[]	O75159	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
185	[]	Q9UJV3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
186	[]	Q9NUQ2	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
187	[]	P16442	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-16	GO_REF:0000041
188	[]	Q9UBQ6	GO:0015012	False	True	[rdfs:subClassOf, BFO:0000050]	-16	GO_REF:0000041
189	[]	P33260	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041
190	[]	P61962	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
191	[]	Q9UHE5	GO:0006749	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
192	[]	Q86Y38	GO:0030206	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
193	[]	P08684	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
194	[]	Q8WXK3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
195	[]	Q92935	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
196	[]	Q9BSL1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
197	[]	Q8N806	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
198	[]	Q6PID8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
199	[]	O14512	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
200	[]	P54886	GO:0055129	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
201	[]	Q9NPI5	GO:0009435	False	True	[rdfs:subClassOf, BFO:0000050]	-18	GO_REF:0000041
202	[]	Q9HB03	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
203	[]	Q7Z6M2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
204	[]	Q8NC69	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
205	[]	Q6ZNI0	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-21	GO_REF:0000041
206	[]	P20711	GO:0042416	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
207	[]	Q8TBE9	GO:0006045	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041
208	[]	Q66K89	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
209	[]	Q9BZQ6	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
210	[]	Q495W5	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-18	GO_REF:0000041
211	[]	O95954	GO:0019556	False	True	[rdfs:subClassOf, BFO:0000050]	-24	GO_REF:0000041
212	[]	O95954	GO:0019557	False	True	[rdfs:subClassOf, BFO:0000050]	-25	GO_REF:0000041
213	[]	P11712	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
214	[]	Q6P3W2	GO:0017183	False	True	[rdfs:subClassOf, BFO:0000050]	-33	GO_REF:0000041
215	[]	Q8WXJ9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
216	[]	Q7L622	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
217	[]	Q8N4N3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
218	[]	O60218	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000041
219	[]	Q12829	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
220	[]	Q9NWZ5	GO:0044206	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041
221	[]	Q9NWZ5	GO:0044211	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041
222	[]	P05091	GO:0006068	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
223	[]	Q13825	GO:0006552	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041
224	[]	Q6PJ21	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
225	[]	Q93088	GO:0006579	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
226	[]	P24298	GO:0042853	False	True	[rdfs:subClassOf, BFO:0000050]	-26	GO_REF:0000041
227	[]	Q96L58	GO:0030206	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
228	[]	Q96L58	GO:0015012	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
229	[]	Q8N5D0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
230	[]	Q96JK2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
231	[]	Q9HBI6	GO:0031408	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
232	[]	Q5T4S7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
233	[]	P27815	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
234	[]	Q8NE62	GO:0019285	False	True	[rdfs:subClassOf, BFO:0000050]	-15	GO_REF:0000041
235	[]	Q03393	GO:0006729	False	True	[rdfs:subClassOf, BFO:0000050]	-25	GO_REF:0000041
236	[]	Q96JP0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
237	[]	Q8NEA9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
238	[]	Q9NWX5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
239	[]	Q6JEL2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
240	[]	Q92947	GO:0006568	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
241	[]	Q53H12	GO:0046486	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
242	[]	Q5TAQ9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
243	[]	Q05516	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
244	[]	Q9UK73	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
245	[]	Q96L50	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
246	[]	P30837	GO:0006068	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
247	[]	Q9UKU7	GO:0006574	False	True	[rdfs:subClassOf, BFO:0000050]	-23	GO_REF:0000041
248	[]	Q9UJM8	GO:0006545	False	True	[rdfs:subClassOf, BFO:0000050]	-17	GO_REF:0000041
249	[]	Q5VXH4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
250	[]	Q6IQ16	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
251	[]	Q9Y2T3	GO:0006147	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
252	[]	Q9HCL2	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
253	[]	A5PLL7	GO:0006631	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
254	[]	Q15345	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
255	[]	P17812	GO:0044210	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
256	[]	Q9Y223	GO:0006045	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041
257	[]	P10635	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
258	[]	Q07343	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
259	[]	P00439	GO:0006559	False	True	[rdfs:subClassOf, BFO:0000050]	-16	GO_REF:0000041
260	[]	Q9H9P5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
261	[]	P32754	GO:0006559	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
262	[]	P46019	GO:0005977	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
263	[]	O94766	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
264	[]	Q4G163	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
265	[]	P31350	GO:0006260	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041
266	[]	Q9Y5Q0	GO:0006665	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041
267	[]	O60658	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
268	[]	Q9Y2U9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
269	[]	Q53GQ0	GO:0006703	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
270	[]	Q53GQ0	GO:0006633	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041
271	[]	C9JR72	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
272	[]	Q9H765	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
273	[]	Q6NUI2	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
274	[]	Q08493	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
275	[]	Q08477	GO:0019369	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
276	[]	O95045	GO:0044206	False	True	[rdfs:subClassOf, BFO:0000050]	-35	GO_REF:0000041
277	[]	O94788	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041
278	[]	Q8WWF5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
279	[]	P52848	GO:0030210	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
280	[]	Q8N9L9	GO:0006633	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
281	[]	Q92523	GO:0006635	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041
282	[]	A8MQ27	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
283	[]	Q86UL3	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
284	[]	Q8NFW8	GO:0006054	False	True	[rdfs:subClassOf, BFO:0000050]	-15	GO_REF:0000041
285	[]	Q9C026	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
286	[]	Q9Y233	GO:0046069	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
287	[]	Q9Y233	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
288	[]	Q86YJ5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
289	[]	Q9NRZ5	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
290	[]	Q13191	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
291	[]	P43353	GO:0006068	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
292	[]	P46020	GO:0005977	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
293	[]	P0DUQ2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
294	[]	Q6YP21	GO:0097053	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
295	[]	Q93100	GO:0005977	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
296	[]	Q58WW2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
297	[]	Q9P2E8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
298	[]	Q6ZVZ8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
299	[]	Q8NDV1	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
300	[]	Q96G25	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
301	[]	P05177	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041
302	[]	Q9H832	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
303	[]	Q13085	GO:2001295	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
304	[]	Q96K19	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
305	[]	Q9NPC3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041
306	[]	Q5T447	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
307	[]	O95263	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041
308	[]	O60476	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041
309	[]	O95864	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
310	[]	Q9UBX8	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041
311	[]	P30793	GO:0035998	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041
312	[]	P29218	GO:0006021	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
313	[]	Q9UL01	GO:0030206	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041
314	[]	Q9UL01	GO:0015012	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
315	[]	O14544	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041
316	[]	Q9NYP7	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
317	[]	Q16773	GO:0097053	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
318	[]	P49419	GO:0019285	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
319	[]	Q8NA82	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041
320	[]	P48637	GO:0006750	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000041
321	[]	P41226	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041
322	[]	Q8WXI3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041
323	[]	Q8NC42	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041

[ ]:

[98]:

mega_df = pd.DataFrame()
for df in dfs_by_ref.values():
    mega_df.append(df)
mega_df

/var/folders/nc/m4tx21912kv1b8nk3zzx9plr0000gn/T/ipykernel_40496/2637639069.py:3: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  mega_df.append(df)

[98]:

[99]:

mega_df = pd.concat(dfs_by_ref.values())
mega_df

[99]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	method
0	[]	Q5VVH2	GO:0003755	None	True	[]	-8	GO_REF:0000003
1	[]	Q53EU6	GO:0102420	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000003
2	[]	O95237	GO:0102279	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000003
3	[]	P22612	GO:0004679	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000003
4	[]	P17516	GO:0035410	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000003
...	...	...	...	...	...	...	...	...
13324	[]	Q8N3I7	GO:0050896	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000043
13325	[]	O15067	GO:0005524	False	True	[rdfs:subClassOf, BFO:0000050]	-16	GO_REF:0000043
13326	[]	O15067	GO:0046872	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000043
13327	[]	A1L3X4	GO:0046872	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000043
13328	[]	P32881	GO:0051607	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000043

71845 rows × 8 columns

[100]:

mega_df.groupby("method").mean(numeric_only=True)

[100]:

	is_deletion	closure_delta
method
GO_REF:0000002	1.0	-6.256293
GO_REF:0000003	1.0	-2.435816
GO_REF:0000041	1.0	-9.901235
GO_REF:0000043	1.0	-5.570560
GO_REF:0000044	1.0	-6.311431
GO_REF:0000104	1.0	-6.020101
GO_REF:0000107	1.0	-7.604500
GO_REF:0000108	1.0	-0.619598
GO_REF:0000116	1.0	-1.849655
GO_REF:0000117	1.0	-5.905660

Unipathway

[104]:

unipathway = dfs_by_ref["GO_REF:0000041"]
add_labels(unipathway)
unipathway

[104]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	method	old_object_label
0	[]	Q53EU6	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
1	[]	Q5VZY2	GO:0006644	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	phospholipid metabolic process
2	[]	P10632	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041	retinol metabolic process
3	[]	Q9NXB9	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	unsaturated fatty acid biosynthetic process
4	[]	Q969V5	GO:0016925	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	protein sumoylation
5	[]	Q9P2W7	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein glycosylation
6	[]	A6NK59	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
7	[]	Q9H1B5	GO:0030206	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	chondroitin sulfate biosynthetic process
8	[]	Q693B1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
9	[]	O60927	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
10	[]	Q8WV16	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
11	[]	Q9UK23	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041	protein glycosylation
12	[]	Q9HAY6	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	retinol metabolic process
13	[]	P30038	GO:0010133	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	proline catabolic process to glutamate
14	[]	P20815	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	retinol metabolic process
15	[]	P11172	GO:0044205	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	'de novo' UMP biosynthetic process
16	[]	Q9H920	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
17	[]	Q8N9I9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
18	[]	Q8TD30	GO:0042853	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	L-alanine catabolic process
19	[]	P43304	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041	glycerol catabolic process
20	[]	Q8WXH6	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
21	[]	Q9NQC1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	protein ubiquitination
22	[]	Q15370	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	protein ubiquitination
23	[]	P22557	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	protoporphyrinogen IX biosynthetic process
24	[]	P08243	GO:0070981	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	L-asparagine biosynthetic process
25	[]	P36957	GO:0033512	False	True	[rdfs:subClassOf, BFO:0000050]	-21	GO_REF:0000041	L-lysine catabolic process to acetyl-CoA via s...
26	[]	P13716	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	protoporphyrinogen IX biosynthetic process
27	[]	P47895	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041	retinol metabolic process
28	[]	Q9NWM0	GO:0046208	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	spermine catabolic process
29	[]	Q8N7A1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
30	[]	Q4G0X4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
31	[]	P33908	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein glycosylation
32	[]	Q8WXK1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
33	[]	O00635	GO:0016925	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	protein sumoylation
34	[]	Q9UI17	GO:0006579	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	amino-acid betaine catabolic process
35	[]	Q9BQ90	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
36	[]	P48448	GO:0006068	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	ethanol catabolic process
37	[]	Q12834	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
38	[]	Q13011	GO:0006635	False	True	[rdfs:subClassOf, BFO:0000050]	-28	GO_REF:0000041	fatty acid beta-oxidation
39	[]	P08397	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	protoporphyrinogen IX biosynthetic process
40	[]	P30566	GO:0006189	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	'de novo' IMP biosynthetic process
41	[]	Q96NS5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
42	[]	A6NNE9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
43	[]	Q8NEB5	GO:0006644	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	phospholipid metabolic process
44	[]	P06132	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	protoporphyrinogen IX biosynthetic process
45	[]	P32189	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	glycerol catabolic process
46	[]	Q86XS8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
47	[]	Q9BSK4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
48	[]	P00352	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	retinol metabolic process
49	[]	Q9Y315	GO:0046386	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	deoxyribose phosphate catabolic process
50	[]	P04181	GO:0055129	False	True	[rdfs:subClassOf, BFO:0000050]	-16	GO_REF:0000041	L-proline biosynthetic process
51	[]	Q6UWP2	GO:0006703	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	estrogen biosynthetic process
52	[]	P24462	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	retinol metabolic process
53	[]	Q92781	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	retinol metabolic process
54	[]	Q15751	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041	protein ubiquitination
55	[]	Q9NRJ4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
56	[]	Q92624	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
57	[]	Q9BY49	GO:0006633	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041	fatty acid biosynthetic process
58	[]	Q96M94	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
59	[]	Q96N76	GO:0019556	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	histidine catabolic process to glutamate and f...
60	[]	Q96N76	GO:0019557	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	histidine catabolic process to glutamate and f...
61	[]	Q6UWP7	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
62	[]	Q9NXF7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
63	[]	Q9BR09	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
64	[]	Q8NBN7	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000041	retinol metabolic process
65	[]	Q6GTS8	GO:0006631	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	fatty acid metabolic process
66	[]	Q9H1B7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
67	[]	Q5VVX9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
68	[]	P55263	GO:0044209	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	AMP salvage
69	[]	Q9NP56	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cAMP catabolic process
70	[]	P20132	GO:0006094	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	gluconeogenesis
71	[]	Q02127	GO:0044205	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041	'de novo' UMP biosynthetic process
72	[]	Q5QP82	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
73	[]	Q99943	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
74	[]	Q9Y4D8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein ubiquitination
75	[]	Q16394	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein glycosylation
76	[]	Q7L273	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
77	[]	P49189	GO:0045329	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	carnitine biosynthetic process
78	[]	P11086	GO:0042418	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	epinephrine biosynthetic process
79	[]	Q9UKT4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
80	[]	P50416	GO:0006635	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041	fatty acid beta-oxidation
81	[]	P0C0E4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
82	[]	P13196	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	protoporphyrinogen IX biosynthetic process
83	[]	Q8N5D6	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein glycosylation
84	[]	Q8IUQ4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
85	[]	Q9BUZ4	GO:0043161	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	proteasome-mediated ubiquitin-dependent protei...
86	[]	Q8TCG5	GO:0006635	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041	fatty acid beta-oxidation
87	[]	Q99618	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
88	[]	Q9NSE2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein ubiquitination
89	[]	Q9BXS1	GO:0050992	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	dimethylallyl diphosphate biosynthetic process
90	[]	P14324	GO:0033384	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	geranyl diphosphate biosynthetic process
91	[]	Q9GZR1	GO:0016925	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	protein sumoylation
92	[]	Q6TDP4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
93	[]	Q99685	GO:0019433	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	triglyceride catabolic process
94	[]	O15524	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein ubiquitination
95	[]	Q8TEB1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
96	[]	O60909	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-17	GO_REF:0000041	protein glycosylation
97	[]	O76074	GO:0046069	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cGMP catabolic process
98	[]	P21673	GO:0009447	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	putrescine catabolic process
99	[]	O15120	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
100	[]	Q9NWW6	GO:0009435	False	True	[rdfs:subClassOf, BFO:0000050]	-18	GO_REF:0000041	NAD biosynthetic process
101	[]	Q8TBB1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
102	[]	Q8WYK0	GO:0006631	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	fatty acid metabolic process
103	[]	Q9H672	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
104	[]	O95749	GO:0033384	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	geranyl diphosphate biosynthetic process
105	[]	O95749	GO:0033386	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	geranylgeranyl diphosphate biosynthetic process
106	[]	O95749	GO:0045337	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	farnesyl diphosphate biosynthetic process
107	[]	Q8TB52	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
108	[]	Q9Y4B6	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	protein ubiquitination
109	[]	P04424	GO:0000050	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	urea cycle
110	[]	P23109	GO:0032264	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	IMP salvage
111	[]	Q9Y575	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
112	[]	Q5H9S7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
113	[]	O95803	GO:0030210	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	heparin biosynthetic process
114	[]	P49675	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	cholesterol metabolic process
115	[]	Q9NRF8	GO:0044210	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	'de novo' CTP biosynthetic process
116	[]	Q8NCN4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	protein ubiquitination
117	[]	Q01432	GO:0032264	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	IMP salvage
118	[]	Q86XP0	GO:0006631	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	fatty acid metabolic process
119	[]	Q96EH8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
120	[]	Q06203	GO:0006189	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	'de novo' IMP biosynthetic process
121	[]	Q16831	GO:0044206	False	True	[rdfs:subClassOf, BFO:0000050]	-29	GO_REF:0000041	UMP salvage
122	[]	Q16719	GO:0097053	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	L-kynurenine catabolic process
123	[]	Q9H0C5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
124	[]	O14508	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein ubiquitination
125	[]	Q6YFQ2	GO:0006119	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	oxidative phosphorylation
126	[]	Q8TBF5	GO:0006506	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	GPI anchor biosynthetic process
127	[]	Q13907	GO:0050992	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	dimethylallyl diphosphate biosynthetic process
128	[]	Q02928	GO:0031408	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	oxylipin biosynthetic process
129	[]	Q8TEB7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
130	[]	P05089	GO:0000050	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	urea cycle
131	[]	Q8N5Z0	GO:0033512	False	True	[rdfs:subClassOf, BFO:0000050]	-40	GO_REF:0000041	L-lysine catabolic process to acetyl-CoA via s...
132	[]	Q8NHY2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
133	[]	P49641	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein glycosylation
134	[]	P10746	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	protoporphyrinogen IX biosynthetic process
135	[]	A8MWK0	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-20	GO_REF:0000041	unsaturated fatty acid biosynthetic process
136	[]	Q9H2A2	GO:0097053	False	True	[rdfs:subClassOf, BFO:0000050]	-23	GO_REF:0000041	L-kynurenine catabolic process
137	[]	Q8WXH5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein ubiquitination
138	[]	O43255	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
139	[]	Q9NRZ7	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
140	[]	Q5XUX0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
141	[]	Q9UKM7	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein glycosylation
142	[]	P37058	GO:0061370	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	testosterone biosynthetic process
143	[]	O00763	GO:2001295	False	True	[rdfs:subClassOf, BFO:0000050]	-24	GO_REF:0000041	malonyl-CoA biosynthetic process
144	[]	Q5T197	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
145	[]	O14543	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein ubiquitination
146	[]	Q14409	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	glycerol catabolic process
147	[]	Q9HBH5	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000041	retinol metabolic process
148	[]	Q16706	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein glycosylation
149	[]	P52849	GO:0030210	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	heparin biosynthetic process
150	[]	O14732	GO:0006021	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	inositol biosynthetic process
151	[]	Q9H477	GO:0019303	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	D-ribose catabolic process
152	[]	Q12882	GO:0019483	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041	beta-alanine biosynthetic process
153	[]	Q5XPI4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
154	[]	Q96NU7	GO:0019556	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	histidine catabolic process to glutamate and f...
155	[]	Q96NU7	GO:0019557	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	histidine catabolic process to glutamate and f...
156	[]	P78540	GO:0000050	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	urea cycle
157	[]	Q96S21	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
158	[]	P22570	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	cholesterol metabolic process
159	[]	Q8IY47	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	protein ubiquitination
160	[]	O60513	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	protein glycosylation
161	[]	Q6P050	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
162	[]	Q86WB0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
163	[]	Q13946	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cAMP catabolic process
164	[]	Q9UDR5	GO:0033512	False	True	[rdfs:subClassOf, BFO:0000050]	-25	GO_REF:0000041	L-lysine catabolic process to acetyl-CoA via s...
165	[]	Q01433	GO:0032264	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	IMP salvage
166	[]	Q9H3R1	GO:0030210	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	heparin biosynthetic process
167	[]	Q08499	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cAMP catabolic process
168	[]	Q9UK99	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
169	[]	P50336	GO:0006782	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	protoporphyrinogen IX biosynthetic process
170	[]	Q9NXK8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
171	[]	Q9NV06	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	protein ubiquitination
172	[]	Q5T6F0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
173	[]	Q9NPZ5	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein glycosylation
174	[]	Q6ZS86	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	glycerol catabolic process
175	[]	Q8IWU9	GO:0042427	False	True	[rdfs:subClassOf, BFO:0000050]	-21	GO_REF:0000041	serotonin biosynthetic process
176	[]	Q14410	GO:0019563	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	glycerol catabolic process
177	[]	P04818	GO:0006235	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	dTTP biosynthetic process
178	[]	Q8IWR1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
179	[]	O60512	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	protein glycosylation
180	[]	P42357	GO:0019556	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	histidine catabolic process to glutamate and f...
181	[]	P42357	GO:0019557	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	histidine catabolic process to glutamate and f...
182	[]	Q9NRD1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
183	[]	Q9NYL5	GO:0006707	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	cholesterol catabolic process
184	[]	O75159	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein ubiquitination
185	[]	Q9UJV3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	protein ubiquitination
186	[]	Q9NUQ2	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
187	[]	P16442	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-16	GO_REF:0000041	protein glycosylation
188	[]	Q9UBQ6	GO:0015012	False	True	[rdfs:subClassOf, BFO:0000050]	-16	GO_REF:0000041	heparan sulfate proteoglycan biosynthetic process
189	[]	P33260	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041	retinol metabolic process
190	[]	P61962	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
191	[]	Q9UHE5	GO:0006749	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	glutathione metabolic process
192	[]	Q86Y38	GO:0030206	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	chondroitin sulfate biosynthetic process
193	[]	P08684	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	cholesterol metabolic process
194	[]	Q8WXK3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
195	[]	Q92935	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein glycosylation
196	[]	Q9BSL1	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
197	[]	Q8N806	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
198	[]	Q6PID8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
199	[]	O14512	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein ubiquitination
200	[]	P54886	GO:0055129	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	L-proline biosynthetic process
201	[]	Q9NPI5	GO:0009435	False	True	[rdfs:subClassOf, BFO:0000050]	-18	GO_REF:0000041	NAD biosynthetic process
202	[]	Q9HB03	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	unsaturated fatty acid biosynthetic process
203	[]	Q7Z6M2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
204	[]	Q8NC69	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
205	[]	Q6ZNI0	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-21	GO_REF:0000041	protein glycosylation
206	[]	P20711	GO:0042416	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	dopamine biosynthetic process
207	[]	Q8TBE9	GO:0006045	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041	N-acetylglucosamine biosynthetic process
208	[]	Q66K89	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	protein ubiquitination
209	[]	Q9BZQ6	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein glycosylation
210	[]	Q495W5	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-18	GO_REF:0000041	protein glycosylation
211	[]	O95954	GO:0019556	False	True	[rdfs:subClassOf, BFO:0000050]	-24	GO_REF:0000041	histidine catabolic process to glutamate and f...
212	[]	O95954	GO:0019557	False	True	[rdfs:subClassOf, BFO:0000050]	-25	GO_REF:0000041	histidine catabolic process to glutamate and f...
213	[]	P11712	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	cholesterol metabolic process
214	[]	Q6P3W2	GO:0017183	False	True	[rdfs:subClassOf, BFO:0000050]	-33	GO_REF:0000041	peptidyl-diphthamide biosynthetic process from...
215	[]	Q8WXJ9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
216	[]	Q7L622	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
217	[]	Q8N4N3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
218	[]	O60218	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000041	retinol metabolic process
219	[]	Q12829	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
220	[]	Q9NWZ5	GO:0044206	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041	UMP salvage
221	[]	Q9NWZ5	GO:0044211	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041	CTP salvage
222	[]	P05091	GO:0006068	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	ethanol catabolic process
223	[]	Q13825	GO:0006552	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041	leucine catabolic process
224	[]	Q6PJ21	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
225	[]	Q93088	GO:0006579	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	amino-acid betaine catabolic process
226	[]	P24298	GO:0042853	False	True	[rdfs:subClassOf, BFO:0000050]	-26	GO_REF:0000041	L-alanine catabolic process
227	[]	Q96L58	GO:0030206	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	chondroitin sulfate biosynthetic process
228	[]	Q96L58	GO:0015012	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	heparan sulfate proteoglycan biosynthetic process
229	[]	Q8N5D0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein ubiquitination
230	[]	Q96JK2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
231	[]	Q9HBI6	GO:0031408	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	oxylipin biosynthetic process
232	[]	Q5T4S7	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
233	[]	P27815	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cAMP catabolic process
234	[]	Q8NE62	GO:0019285	False	True	[rdfs:subClassOf, BFO:0000050]	-15	GO_REF:0000041	glycine betaine biosynthetic process from choline
235	[]	Q03393	GO:0006729	False	True	[rdfs:subClassOf, BFO:0000050]	-25	GO_REF:0000041	tetrahydrobiopterin biosynthetic process
236	[]	Q96JP0	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
237	[]	Q8NEA9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
238	[]	Q9NWX5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
239	[]	Q6JEL2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
240	[]	Q92947	GO:0006568	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	tryptophan metabolic process
241	[]	Q53H12	GO:0046486	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	glycerolipid metabolic process
242	[]	Q5TAQ9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
243	[]	Q05516	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	protein ubiquitination
244	[]	Q9UK73	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
245	[]	Q96L50	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
246	[]	P30837	GO:0006068	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	ethanol catabolic process
247	[]	Q9UKU7	GO:0006574	False	True	[rdfs:subClassOf, BFO:0000050]	-23	GO_REF:0000041	valine catabolic process
248	[]	Q9UJM8	GO:0006545	False	True	[rdfs:subClassOf, BFO:0000050]	-17	GO_REF:0000041	glycine biosynthetic process
249	[]	Q5VXH4	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
250	[]	Q6IQ16	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
251	[]	Q9Y2T3	GO:0006147	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	guanine catabolic process
252	[]	Q9HCL2	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
253	[]	A5PLL7	GO:0006631	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	fatty acid metabolic process
254	[]	Q15345	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
255	[]	P17812	GO:0044210	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	'de novo' CTP biosynthetic process
256	[]	Q9Y223	GO:0006045	False	True	[rdfs:subClassOf, BFO:0000050]	-8	GO_REF:0000041	N-acetylglucosamine biosynthetic process
257	[]	P10635	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	cholesterol metabolic process
258	[]	Q07343	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cAMP catabolic process
259	[]	P00439	GO:0006559	False	True	[rdfs:subClassOf, BFO:0000050]	-16	GO_REF:0000041	L-phenylalanine catabolic process
260	[]	Q9H9P5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
261	[]	P32754	GO:0006559	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	L-phenylalanine catabolic process
262	[]	P46019	GO:0005977	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	glycogen metabolic process
263	[]	O94766	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein glycosylation
264	[]	Q4G163	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
265	[]	P31350	GO:0006260	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041	DNA replication
266	[]	Q9Y5Q0	GO:0006665	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041	sphingolipid metabolic process
267	[]	O60658	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cAMP catabolic process
268	[]	Q9Y2U9	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
269	[]	Q53GQ0	GO:0006703	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	estrogen biosynthetic process
270	[]	Q53GQ0	GO:0006633	False	True	[rdfs:subClassOf, BFO:0000050]	-11	GO_REF:0000041	fatty acid biosynthetic process
271	[]	C9JR72	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
272	[]	Q9H765	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
273	[]	Q6NUI2	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
274	[]	Q08493	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cAMP catabolic process
275	[]	Q08477	GO:0019369	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	arachidonic acid metabolic process
276	[]	O95045	GO:0044206	False	True	[rdfs:subClassOf, BFO:0000050]	-35	GO_REF:0000041	UMP salvage
277	[]	O94788	GO:0042572	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000041	retinol metabolic process
278	[]	Q8WWF5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
279	[]	P52848	GO:0030210	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	heparin biosynthetic process
280	[]	Q8N9L9	GO:0006633	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	fatty acid biosynthetic process
281	[]	Q92523	GO:0006635	False	True	[rdfs:subClassOf, BFO:0000050]	-14	GO_REF:0000041	fatty acid beta-oxidation
282	[]	A8MQ27	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
283	[]	Q86UL3	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
284	[]	Q8NFW8	GO:0006054	False	True	[rdfs:subClassOf, BFO:0000050]	-15	GO_REF:0000041	N-acetylneuraminate metabolic process
285	[]	Q9C026	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
286	[]	Q9Y233	GO:0046069	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cGMP catabolic process
287	[]	Q9Y233	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cAMP catabolic process
288	[]	Q86YJ5	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
289	[]	Q9NRZ5	GO:0016024	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	CDP-diacylglycerol biosynthetic process
290	[]	Q13191	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	protein ubiquitination
291	[]	P43353	GO:0006068	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	ethanol catabolic process
292	[]	P46020	GO:0005977	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	glycogen metabolic process
293	[]	P0DUQ2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
294	[]	Q6YP21	GO:0097053	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	L-kynurenine catabolic process
295	[]	Q93100	GO:0005977	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	glycogen metabolic process
296	[]	Q58WW2	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	protein ubiquitination
297	[]	Q9P2E8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
298	[]	Q6ZVZ8	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
299	[]	Q8NDV1	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	protein glycosylation
300	[]	Q96G25	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	protein ubiquitination
301	[]	P05177	GO:0008203	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000041	cholesterol metabolic process
302	[]	Q9H832	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
303	[]	Q13085	GO:2001295	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	malonyl-CoA biosynthetic process
304	[]	Q96K19	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
305	[]	Q9NPC3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-7	GO_REF:0000041	protein ubiquitination
306	[]	Q5T447	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
307	[]	O95263	GO:0006198	False	True	[rdfs:subClassOf, BFO:0000050]	-46	GO_REF:0000041	cAMP catabolic process
308	[]	O60476	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-9	GO_REF:0000041	protein glycosylation
309	[]	O95864	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	unsaturated fatty acid biosynthetic process
310	[]	Q9UBX8	GO:0006486	False	True	[rdfs:subClassOf, BFO:0000050]	-10	GO_REF:0000041	protein glycosylation
311	[]	P30793	GO:0035998	False	True	[rdfs:subClassOf, BFO:0000050]	-6	GO_REF:0000041	7,8-dihydroneopterin 3'-triphosphate biosynthe...
312	[]	P29218	GO:0006021	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	inositol biosynthetic process
313	[]	Q9UL01	GO:0030206	False	True	[rdfs:subClassOf, BFO:0000050]	-2	GO_REF:0000041	chondroitin sulfate biosynthetic process
314	[]	Q9UL01	GO:0015012	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	heparan sulfate proteoglycan biosynthetic process
315	[]	O14544	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination
316	[]	Q9NYP7	GO:0006636	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	unsaturated fatty acid biosynthetic process
317	[]	Q16773	GO:0097053	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	L-kynurenine catabolic process
318	[]	P49419	GO:0019285	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	glycine betaine biosynthetic process from choline
319	[]	Q8NA82	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-13	GO_REF:0000041	protein ubiquitination
320	[]	P48637	GO:0006750	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000041	glutathione biosynthetic process
321	[]	P41226	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000041	protein ubiquitination
322	[]	Q8WXI3	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	protein ubiquitination
323	[]	Q8NC42	GO:0016567	False	True	[rdfs:subClassOf, BFO:0000050]	-5	GO_REF:0000041	protein ubiquitination

[105]:

pd.set_option('display.max_rows', 1000)
unipathway.groupby(lbl).min(numeric_only=True).sort_values("closure_delta")

[105]:

		old_object_obsolete	is_deletion	closure_delta
old_object	old_object_label
GO:0046069	cGMP catabolic process	False	True	-46
GO:0006506	GPI anchor biosynthetic process	False	True	-46
GO:0006198	cAMP catabolic process	False	True	-46
GO:0033512	L-lysine catabolic process to acetyl-CoA via saccharopine	False	True	-40
GO:0044206	UMP salvage	False	True	-35
GO:0017183	peptidyl-diphthamide biosynthetic process from peptidyl-histidine	False	True	-33
GO:0006635	fatty acid beta-oxidation	False	True	-28
GO:0042853	L-alanine catabolic process	False	True	-26
GO:0019557	histidine catabolic process to glutamate and formate	False	True	-25
GO:0006729	tetrahydrobiopterin biosynthetic process	False	True	-25
GO:0019556	histidine catabolic process to glutamate and formamide	False	True	-24
GO:2001295	malonyl-CoA biosynthetic process	False	True	-24
GO:0006574	valine catabolic process	False	True	-23
GO:0097053	L-kynurenine catabolic process	False	True	-23
GO:0006486	protein glycosylation	False	True	-21
GO:0042427	serotonin biosynthetic process	False	True	-21
GO:0006636	unsaturated fatty acid biosynthetic process	False	True	-20
GO:0009435	NAD biosynthetic process	False	True	-18
GO:0006545	glycine biosynthetic process	False	True	-17
GO:0055129	L-proline biosynthetic process	False	True	-16
GO:0006559	L-phenylalanine catabolic process	False	True	-16
GO:0015012	heparan sulfate proteoglycan biosynthetic process	False	True	-16
GO:0006054	N-acetylneuraminate metabolic process	False	True	-15
GO:0019285	glycine betaine biosynthetic process from choline	False	True	-15
GO:0019483	beta-alanine biosynthetic process	False	True	-14
GO:0044211	CTP salvage	False	True	-14
GO:0019563	glycerol catabolic process	False	True	-14
GO:0006633	fatty acid biosynthetic process	False	True	-14
GO:0016567	protein ubiquitination	False	True	-13
GO:0006707	cholesterol catabolic process	False	True	-13
GO:0006068	ethanol catabolic process	False	True	-12
GO:0045329	carnitine biosynthetic process	False	True	-12
GO:0061370	testosterone biosynthetic process	False	True	-12
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	False	True	-12
GO:0044205	'de novo' UMP biosynthetic process	False	True	-11
GO:0006552	leucine catabolic process	False	True	-11
GO:0033386	geranylgeranyl diphosphate biosynthetic process	False	True	-10
GO:0030206	chondroitin sulfate biosynthetic process	False	True	-10
GO:0033384	geranyl diphosphate biosynthetic process	False	True	-10
GO:0045337	farnesyl diphosphate biosynthetic process	False	True	-10
GO:0019303	D-ribose catabolic process	False	True	-10
GO:0042572	retinol metabolic process	False	True	-10
GO:0000050	urea cycle	False	True	-10
GO:0005977	glycogen metabolic process	False	True	-9
GO:0006119	oxidative phosphorylation	False	True	-9
GO:0006703	estrogen biosynthetic process	False	True	-9
GO:0006235	dTTP biosynthetic process	False	True	-8
GO:0009447	putrescine catabolic process	False	True	-8
GO:0006045	N-acetylglucosamine biosynthetic process	False	True	-8
GO:0006094	gluconeogenesis	False	True	-8
GO:0006568	tryptophan metabolic process	False	True	-8
GO:0031408	oxylipin biosynthetic process	False	True	-8
GO:0006579	amino-acid betaine catabolic process	False	True	-7
GO:0030210	heparin biosynthetic process	False	True	-7
GO:0006631	fatty acid metabolic process	False	True	-7
GO:0008203	cholesterol metabolic process	False	True	-6
GO:0070981	L-asparagine biosynthetic process	False	True	-6
GO:0035998	7,8-dihydroneopterin 3'-triphosphate biosynthetic process	False	True	-6
GO:0042416	dopamine biosynthetic process	False	True	-6
GO:0032264	IMP salvage	False	True	-6
GO:0006021	inositol biosynthetic process	False	True	-5
GO:0010133	proline catabolic process to glutamate	False	True	-5
GO:0006260	DNA replication	False	True	-4
GO:0006665	sphingolipid metabolic process	False	True	-4
GO:0016925	protein sumoylation	False	True	-3
GO:0019369	arachidonic acid metabolic process	False	True	-3
GO:0006189	'de novo' IMP biosynthetic process	False	True	-3
GO:0006147	guanine catabolic process	False	True	-3
GO:0019433	triglyceride catabolic process	False	True	-2
GO:0006782	protoporphyrinogen IX biosynthetic process	False	True	-2
GO:0050992	dimethylallyl diphosphate biosynthetic process	False	True	-2
GO:0046386	deoxyribose phosphate catabolic process	False	True	-2
GO:0042418	epinephrine biosynthetic process	False	True	-2
GO:0016024	CDP-diacylglycerol biosynthetic process	False	True	-2
GO:0006644	phospholipid metabolic process	False	True	-2
GO:0046208	spermine catabolic process	False	True	-2
GO:0046486	glycerolipid metabolic process	False	True	-1
GO:0006749	glutathione metabolic process	False	True	-1
GO:0044210	'de novo' CTP biosynthetic process	False	True	-1
GO:0044209	AMP salvage	False	True	-1
GO:0006750	glutathione biosynthetic process	False	True	0

[108]:

unipathway.query("old_object == 'GO:0042853'")

[108]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	method	old_object_label
18	[]	Q8TD30	GO:0042853	False	True	[rdfs:subClassOf, BFO:0000050]	-12	GO_REF:0000041	L-alanine catabolic process
226	[]	P24298	GO:0042853	False	True	[rdfs:subClassOf, BFO:0000050]	-26	GO_REF:0000041	L-alanine catabolic process

Difference across species

[134]:

human = mega_df

[129]:

def analyze_gaf(gaf_path):
    species_df = gaf2df(gaf_path)
    print(len(species_df))
    by_ref = {}
    dfs = []
    for goref in gorefs:
        print(goref)
        df = analyze_iea(species_df, goref)
        print(len(df))
        df['method'] = goref
        dfs.append(df)
    all_df = pd.concat(dfs)
    return all_df

[124]:

sgd_gaf = gaf2df("input/sgd.gaf")

[125]:

sgd_gaf

[125]:

	db	local_id	db_object_symbol	qualifiers	ontology_class_ref	supporting_references	evidence_type	with_or_from	aspect	db_object_name	db_object_synonyms	db_object_type	db_object_taxon	annotation_date	assigned_by	annotation_extensions	gene_product_form
0	SGD	S000000735	GCN4	involved_in	GO:1990139	PMID:31211995	IMP	NaN	P	bZIP transcriptional activator of amino acid b...	YEL009C\|AAS3\|ARG9\|AAS101\|amino acid starvation...	protein	taxon:559292	20200206	SGD	NaN	UniProtKB:P03069
1	SGD	S000003026	RAD6	contributes_to	GO:0017116	PMID:9287349	IDA	NaN	F	Ubiquitin-conjugating enzyme (E2)	YGL058W\|PSO8\|UBC2\|E2 ubiquitin-conjugating pro...	protein	taxon:559292	20131012	SGD	part_of(GO:0097505)	UniProtKB:P06104
2	SGD	S000001503	SPT23	enables	GO:0003674	GO_REF:0000015	ND	NaN	F	ER membrane protein involved in regulation of ...	YKL020C	protein	taxon:559292	20181102	SGD	NaN	UniProtKB:P35210
3	SGD	S000028746	FMP49	located_in	GO:0005739	PMID:14576278	HDA	NaN	C	Mitochondrial protein of unknown function	YER038W-A	protein	taxon:559292	20040923	SGD	NaN	UniProtKB:A0A023PZB3
4	SGD	S000005730	DED1	enables	GO:0003724	PMID:10364207	IDA	NaN	F	ATP-dependent DEAD-box RNA helicase with stran...	YOR204W\|SPP81\|DEAD-box ATP-dependent RNA helic...	protein	taxon:559292	20090529	SGD	NaN	UniProtKB:P06634
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
121507	SGD	S000000871	ARG56	enables	GO:0003942	PMID:21873635	IBA	PANTHER:PTN001155520\|PomBase:SPAC4G9.09c\|SGD:S...	F	bifunctional acetylglutamate kinase/N-acetyl-g...	ARG56\|YER069W	protein	taxon:559292	20170228	GO_Central	NaN	NaN
121508	SGD	S000003824	RPA12	contributes_to	GO:0001054	PMID:21873635	IBA	PANTHER:PTN000133053\|SGD:S000003824	F	DNA-directed RNA polymerase I core subunit RPA12	RPA12\|RRN4\|YJR063W	protein	taxon:559292	20170228	GO_Central	NaN	NaN
121509	SGD	S000006377	VPS4	involved_in	GO:0016197	PMID:21873635	IBA	PANTHER:PTN000553912\|UniProtKB:Q9UN37\|PomBase:...	P	AAA family ATPase VPS4	VPS4\|VPL4\|VPT10\|DID6\|CSC1\|END13\|GRD13\|YPR173C	protein	taxon:559292	20221008	GO_Central	NaN	NaN
121510	SGD	S000001412	MCM10	enables	GO:0003688	PMID:21873635	IBA	PANTHER:PTN000335708\|SGD:S000001412	F	NaN	MCM10\|DNA43\|YIL150C	protein	taxon:559292	20170228	GO_Central	NaN	NaN
121511	SGD	S000001776	BET3	is_active_in	GO:0033106	PMID:21873635	IBA	PANTHER:PTN000316141\|SGD:S000001776	C	TRAPP complex core subunit BET3	BET3\|YKR068C	protein	taxon:559292	20170602	GO_Central	NaN	NaN

121512 rows × 17 columns

[126]:

sgd_foo = analyze_iea(sgd_gaf, "GO_REF:0000002")

[128]:

sgd_foo["method"] = "GO_REF:0000002"
sgd_foo

[128]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	method
0	[]	S000005069	GO:0022857	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000002
1	[]	S000005069	GO:0055085	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000002
2	[]	S000006233	GO:0016192	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000002
3	[]	S000006233	GO:0030117	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000002
4	[]	S000006233	GO:0006886	False	True	[rdfs:subClassOf, BFO:0000050]	-1	GO_REF:0000002
...	...	...	...	...	...	...	...	...
3743	[]	S000005730	GO:0003676	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000002
3744	[]	S000001208	GO:0000398	False	True	[rdfs:subClassOf, BFO:0000050]	0	GO_REF:0000002
3745	[]	S000001208	GO:0008237	False	True	[rdfs:subClassOf, BFO:0000050]	-4	GO_REF:0000002
3746	[]	S000001208	GO:0008233	False	True	[rdfs:subClassOf, BFO:0000050]	-3	GO_REF:0000002
3747	[]	S000000418	GO:0030071	False	True	[rdfs:subClassOf, BFO:0000050]	-15	GO_REF:0000002

3748 rows × 8 columns

[130]:

sgd = analyze_gaf("input/sgd.gaf")

121512
GO_REF:0000003
362
GO_REF:0000044
1040
GO_REF:0000002
3748
GO_REF:0000116
0
GO_REF:0000117
1587
GO_REF:0000107
0
GO_REF:0000108
1028
GO_REF:0000041
186
GO_REF:0000104
127
GO_REF:0000043
11559

[131]:

type(sgd)

[131]:

pandas.core.frame.DataFrame

[132]:

sgd

[132]:

	publications	subject	old_object	old_object_obsolete	is_deletion	closure_predicates	closure_delta	method
0	[]	S000002424	GO:0052724	False	True	[rdfs:subClassOf, BFO:0000050]	-1.0	GO_REF:0000003
1	[]	S000002424	GO:0000832	False	True	[rdfs:subClassOf, BFO:0000050]	-1.0	GO_REF:0000003
2	[]	S000002424	GO:0052723	False	True	[rdfs:subClassOf, BFO:0000050]	-1.0	GO_REF:0000003
3	[]	S000005313	GO:0052917	False	True	[rdfs:subClassOf, BFO:0000050]	-1.0	GO_REF:0000003
4	[]	S000002650	GO:0043864	False	True	[rdfs:subClassOf, BFO:0000050]	-3.0	GO_REF:0000003
...	...	...	...	...	...	...	...	...
11554	[]	S000005749	GO:0006897	False	True	[rdfs:subClassOf, BFO:0000050]	-5.0	GO_REF:0000043
11555	[]	S000005749	GO:0015031	False	True	[rdfs:subClassOf, BFO:0000050]	-12.0	GO_REF:0000043
11556	[]	S000001208	GO:0006397	False	True	[rdfs:subClassOf, BFO:0000050]	0.0	GO_REF:0000043
11557	[]	S000001208	GO:0008380	False	True	[rdfs:subClassOf, BFO:0000050]	0.0	GO_REF:0000043
11558	[]	S000001208	GO:1990904	False	True	[rdfs:subClassOf, BFO:0000050]	0.0	GO_REF:0000043

19637 rows × 8 columns

[133]:

sgd.groupby("method").mean(numeric_only=True)

[133]:

	closure_delta
method
GO_REF:0000002	-2.113661
GO_REF:0000003	-1.919890
GO_REF:0000041	-5.155914
GO_REF:0000043	-1.074228
GO_REF:0000044	-2.593269
GO_REF:0000104	-3.551181
GO_REF:0000108	-0.389105
GO_REF:0000117	-0.192817

[135]:

human.groupby("method").mean(numeric_only=True)

[135]:

	is_deletion	closure_delta
method
GO_REF:0000002	1.0	-6.256293
GO_REF:0000003	1.0	-2.435816
GO_REF:0000041	1.0	-9.901235
GO_REF:0000043	1.0	-5.570560
GO_REF:0000044	1.0	-6.311431
GO_REF:0000104	1.0	-6.020101
GO_REF:0000107	1.0	-7.604500
GO_REF:0000108	1.0	-0.619598
GO_REF:0000116	1.0	-1.849655
GO_REF:0000117	1.0	-5.905660

[136]:

human["species"] = "human"
sgd["species"] = "yeast"

[138]:

all_df = pd.concat([human, sgd])

/var/folders/nc/m4tx21912kv1b8nk3zzx9plr0000gn/T/ipykernel_40496/2618427164.py:1: FutureWarning: In a future version, object-dtype columns with all-bool values will not be included in reductions with bool_only=True. Explicitly cast to bool dtype instead.
  all_df = pd.concat([human, sgd])

[140]:

smry = all_df.groupby(["species", "method"]).mean(numeric_only=True)
smry

[140]:

		closure_delta
species	method
human	GO_REF:0000002	-6.256293
	GO_REF:0000003	-2.435816
	GO_REF:0000041	-9.901235
	GO_REF:0000043	-5.570560
	GO_REF:0000044	-6.311431
	GO_REF:0000104	-6.020101
	GO_REF:0000107	-7.604500
	GO_REF:0000108	-0.619598
	GO_REF:0000116	-1.849655
	GO_REF:0000117	-5.905660
yeast	GO_REF:0000002	-2.113661
	GO_REF:0000003	-1.919890
	GO_REF:0000041	-5.155914
	GO_REF:0000043	-1.074228
	GO_REF:0000044	-2.593269
	GO_REF:0000104	-3.551181
	GO_REF:0000108	-0.389105
	GO_REF:0000117	-0.192817

[143]:

smry.

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[143], line 1
----> 1 smry.names

File ~/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pandas/core/generic.py:5902, in NDFrame.__getattr__(self, name)
   5895 if (
   5896     name not in self._internal_names_set
   5897     and name not in self._metadata
   5898     and name not in self._accessors
   5899     and self._info_axis._can_hold_identifiers_and_holds_name(name)
   5900 ):
   5901     return self[name]
-> 5902 return object.__getattribute__(self, name)

AttributeError: 'DataFrame' object has no attribute 'names'

[144]:

pombase = analyze_gaf("input/pombase.gaf")

54542
GO_REF:0000003
76
GO_REF:0000044
52
GO_REF:0000002
968
GO_REF:0000116
165
GO_REF:0000117
57
GO_REF:0000107
0
GO_REF:0000108
0
GO_REF:0000041
64
GO_REF:0000104
124
GO_REF:0000043
518

[145]:

pombase.groupby("method").mean(numeric_only=True)

[145]:

	closure_delta
method
GO_REF:0000002	-5.535124
GO_REF:0000003	-1.815789
GO_REF:0000041	-10.796875
GO_REF:0000043	-10.403475
GO_REF:0000044	-4.615385
GO_REF:0000104	-5.669355
GO_REF:0000116	-3.793939
GO_REF:0000117	-6.228070

[153]:

pombase["species"] = "pombe"
all_df = pd.concat([human, sgd, pombase])

/var/folders/nc/m4tx21912kv1b8nk3zzx9plr0000gn/T/ipykernel_40496/747263277.py:2: FutureWarning: In a future version, object-dtype columns with all-bool values will not be included in reductions with bool_only=True. Explicitly cast to bool dtype instead.
  all_df = pd.concat([human, sgd, pombase])

[154]:

all_df.groupby(["species", "method"]).mean(numeric_only=True)

[154]:

		closure_delta
species	method
human	GO_REF:0000002	-6.256293
	GO_REF:0000003	-2.435816
	GO_REF:0000041	-9.901235
	GO_REF:0000043	-5.570560
	GO_REF:0000044	-6.311431
	GO_REF:0000104	-6.020101
	GO_REF:0000107	-7.604500
	GO_REF:0000108	-0.619598
	GO_REF:0000116	-1.849655
	GO_REF:0000117	-5.905660
pombe	GO_REF:0000002	-5.535124
	GO_REF:0000003	-1.815789
	GO_REF:0000041	-10.796875
	GO_REF:0000043	-10.403475
	GO_REF:0000044	-4.615385
	GO_REF:0000104	-5.669355
	GO_REF:0000116	-3.793939
	GO_REF:0000117	-6.228070
yeast	GO_REF:0000002	-2.113661
	GO_REF:0000003	-1.919890
	GO_REF:0000041	-5.155914
	GO_REF:0000043	-1.074228
	GO_REF:0000044	-2.593269
	GO_REF:0000104	-3.551181
	GO_REF:0000108	-0.389105
	GO_REF:0000117	-0.192817

[169]:

all_df.groupby(["species", "method"]).sum(numeric_only=True)

[169]:

		closure_delta
species	method
human	GO_REF:0000002	-39521.0
	GO_REF:0000003	-1537.0
	GO_REF:0000041	-3208.0
	GO_REF:0000043	-74250.0
	GO_REF:0000044	-50908.0
	GO_REF:0000104	-1198.0
	GO_REF:0000107	-294720.0
	GO_REF:0000108	-2036.0
	GO_REF:0000116	-1341.0
	GO_REF:0000117	-1252.0
pombe	GO_REF:0000002	-5358.0
	GO_REF:0000003	-138.0
	GO_REF:0000041	-691.0
	GO_REF:0000043	-5389.0
	GO_REF:0000044	-240.0
	GO_REF:0000104	-703.0
	GO_REF:0000116	-626.0
	GO_REF:0000117	-355.0
yeast	GO_REF:0000002	-7922.0
	GO_REF:0000003	-695.0
	GO_REF:0000041	-959.0
	GO_REF:0000043	-12417.0
	GO_REF:0000044	-2697.0
	GO_REF:0000104	-451.0
	GO_REF:0000108	-400.0
	GO_REF:0000117	-306.0

[167]:

smry = all_df.groupby(["species", "method"]).sum(numeric_only=True) / all_df.groupby(["species"]).sum(numeric_only=True)
smry

[167]:

		closure_delta
species	method
human	GO_REF:0000002	0.084092
	GO_REF:0000003	0.003270
	GO_REF:0000041	0.006826
	GO_REF:0000043	0.157988
	GO_REF:0000044	0.108322
	GO_REF:0000104	0.002549
	GO_REF:0000107	0.627103
	GO_REF:0000108	0.004332
	GO_REF:0000116	0.002853
	GO_REF:0000117	0.002664
pombe	GO_REF:0000002	0.396889
	GO_REF:0000003	0.010222
	GO_REF:0000041	0.051185
	GO_REF:0000043	0.399185
	GO_REF:0000044	0.017778
	GO_REF:0000104	0.052074
	GO_REF:0000116	0.046370
	GO_REF:0000117	0.026296
yeast	GO_REF:0000002	0.306496
	GO_REF:0000003	0.026889
	GO_REF:0000041	0.037103
	GO_REF:0000043	0.480404
	GO_REF:0000044	0.104345
	GO_REF:0000104	0.017449
	GO_REF:0000108	0.015476
	GO_REF:0000117	0.011839

[168]:

import seaborn

pivot = smry.reset_index().pivot(index="method", columns="species", values="closure_delta")
seaborn.heatmap(pivot, annot=True, fmt=".2f")

[168]:

<Axes: xlabel='species', ylabel='method'>

../../../_images/examples_Ontologies_GO_Annotation-Contributions_70_1.png

[159]:

c.META.foo

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[159], line 1
----> 1 c.META.foo

AttributeError: 'dict' object has no attribute 'foo'

[ ]: