Labels from xrefs being used as term label

[Robbie1977]

This Affects GO and SO in VFB:
The SO ones are easiest to spot:

c.label	c.label_rdfs[0]	c.short_form
56	"wiki"	"wild_type"
57	"wiki"	"syntenic"
58	"wiki"	"orthologous_region"
59	"wiki"	"paralogous_region"
60	"wiki"	"rolling_circle"
61	"wiki"	"insertion_sequence"
62	"wiki"	"vault_RNA"
63	"wiki"	"Y_RNA"
64	"wiki"	"twintron"
65	"wiki"	"cytosolic_18S_rRNA"
66	"wiki"	"vector_replicon"
67	"wiki"	"signal_peptide"
68	"wiki"	"restriction_fragment"
69	"wiki"	"tmRNA"
70	"wiki"	"group_I_intron"
71	"wiki"	"Hoogsteen_base_pair"
72	"wiki"	"retrotransposed"
73	"wiki"	"Shine_Dalgarno_sequence"
74	"wiki"	"helitron"
75	"wiki"	"intergenic_region"
76	"wiki"	"oligo"
77	"wiki"	"siRNA"
78	"wiki"	"minisatellite"
79	"wiki"	"antisense_RNA"
80	"wiki"	"polycistronic_mRNA"
81	"wiki"	"telomere"
82	"wiki"	"insulator"
83	"wiki"	"A_box"
84	"Insertion"	"insertion"
85	"wiki"	"dispersed_repeat"
86	"cytosolic_SSU_rRNA"	"small_subunit_rRNA"
87	"wiki"	"cytosolic_28S_rRNA"
88	"wiki"	"ncRNA"
89	"wiki"	"oriT"
90	"wiki"	"intein"
91	"wiki"	"DNA_motif"
92	"wiki"	"cDNA"
93	"wiki"	"plasmid_vector"
94	"wiki"	"kinetoplast"
95	"wiki"	"predicted"
96	"wiki"	"genomic_island"
97	"wiki"	"G_quartet"
98	"wiki"	"satellite_DNA"
99	"wiki"	"locus_control_region"
100	"wiki"	"K_turn_RNA_motif"
101	"wiki"	"nuclear_gene"
102	"wiki"	"mt_gene"
103	"wiki"	"antisense"
104	"wiki"	"probe"
105	"wiki"	"aneuploid"
106	"wiki"	"hyperploid"
107	"wiki"	"operator"
108	"wiki"	"transposable_element"
109	"wiki"	"promoter"
110	"wiki"	"clone"
111	"wiki"	"phagemid"
112	"wiki"	"fosmid"
113	"wiki"	"terminator"
114	"wiki"	"exon"
115	"wiki"	"genomically_imprinted"
116	"wiki"	"RFLP_fragment"
117	"wiki"	"retrotransposon"
118	"wiki"	"CAAT_signal"
119	"wiki"	"TATA_box"
120	"wiki"	"minus_10_signal"
121	"wiki"	"operon"
122	"wiki"	"mature_transcript"
123	"wiki"	"mRNA"
124	"wiki"	"fusion_gene"
125	"wiki"	"microsatellite"
126	"wiki"	"snRNA"
127	"wiki"	"miRNA"
128	"wiki"	"SINE_element"
129	"WIKI"	"simple_sequence_length_variation"
130	"wiki"	"five_prime_UTR"
131	"wiki"	"origin_of_replication"
132	"wiki"	"D_loop"
133	"wiki"	"integron"
134	"wiki"	"floxed"
135	"wiki"	"chromosome"
136	"wiki"	"telomerase_RNA"
137	"wiki"	"U1_snRNA"
138	"wiki"	"U2_snRNA"
139	"wiki"	"U5_snRNA"
140	"wiki"	"U11_snRNA"
141	"wiki"	"U12_snRNA"
142	"wiki"	"MicF_RNA"
143	"wiki"	"OxyS_RNA"
144	"wiki"	"spot_42_RNA"
145	"wiki"	"ribozyme"
146	"wiki"	"cytosolic_5_8S_rRNA"
147	"wiki"	"GcvB_RNA"
148	"wiki"	"start_codon"
149	"wiki"	"direct_repeat"
150	"wiki"	"CpG_island"
151	"Tret1"	"Tret1-1"
152	"wiki"	"synonymous_variant"
153	"wiki"	"AFLP_fragment"
154	"VAT"	"inframe_insertion"
155	"wiki"	"lysidine"
156	"Initiating Methionine"	"initiator_codon_variant"
157	"Frameshift"	"frameshift_variant"
158	"VAT"	"structural_variant"
159	"reference genome sequence"	"reference_genome"
160	"wikipedia"	"sequence_motif"
161	"wiki"	"wobble_base_pair"
162	"wiki"	"silent_mutation"
163	"wiki"	"epitope"
164	"wiki"	"tetraloop"
165	"wiki"	"phage_sequence"
166	"wiki"	"piRNA"
167	"wiki"	"genotype"
168	"wiki"	"post_translationally_modified_region"
169	"wiki"	"coiled_coil"
170	"wiki"	"polypeptide_structural_motif"
171	"wiki"	"three_ten_helix"
172	"wiki"	"beta_strand"
173	"wiki"	"pi_helix"
174	"wiki"	"alpha_helix"
175	"wiki"	"TNA_oligo"
176	"wiki"	"GNA_oligo"
177	"wiki"	"AU_rich_element"
178	"wiki"	"LNA_oligo"
179	"wiki"	"translational_frameshift"
180	"wiki"	"group_III_intron"
181	"wiki"	"autopolyploid"
182	"wiki"	"polyploid"
183	"wiki"	"assembly"
184	"wiki"	"mobile"
185	"wiki"	"amino_acid"
186	"wiki"	"base"
187	"wiki"	"pseudouridine"
188	"wiki"	"primer_binding_site"
189	"wiki"	"gene_cassette"
190	"wiki"	"regulatory_region"

@Clare72 has spotted this before having the label on the xrefs seems to cause this issue on scRNAseq data

[dosumis]

@hkir-dev - this appears to be hitting us too:

Becomes

[dosumis]

Yet another example - this time from CL:

[dosumis]

CC @ubyndr

[hkir-dev]

This issue has been resolved in a forked repository: OBASKTools#2.

The same fix can be applied to this repository as well.

[dosumis]

@Robbie1977 - Fix is working now for us. Do you want to pull back into your version, or switch to using the OBASK version for VFB.

[Robbie1977]

@dosumis I'm going to try an update after this load; do you have a compiled release?

[dosumis]

@ubyndr does

[ubyndr]

Hi @Robbie1977 , you can find the jar file here, owl2neo4jcsv.jar

[hkir-dev]

I just want to note that there may be significant differences between the fork and the original repository, so the JAR generated from the fork could potentially break the VFB pipeline.