low hanging build/load error messages

[turbomam]

Patterns

• [ ] INFO:root:class "chemical entity" slot "chemical formula" does not reference an existing slot. New slot was created.
• [x] INFO:root:Default_range not specified. Default set to 'string'
• [x] Unrecognized prefix: COG
• [x] WARNING:root:File "", someline/somecol: Prefix case mismatch - supplied: MIXS expected: mixs
• [ ] WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/FunctionalAnnotation

This duplicates a few other issues

• 234

• 232

• 103

[turbomam]

Verbose

INFO:root:class "chemical entity" slot "chemical formula" does not reference an existing slot.  New slot was created.
INFO:root:class "chemical entity" slot "inchi key" does not reference an existing slot.  New slot was created.
INFO:root:class "chemical entity" slot "inchi" does not reference an existing slot.  New slot was created.
INFO:root:class "chemical entity" slot "smiles" does not reference an existing slot.  New slot was created.
INFO:root:class "database" slot "date created" does not reference an existing slot.  New slot was created.
INFO:root:class "database" slot "etl software version" does not reference an existing slot.  New slot was created.
INFO:root:class "database" slot "nmdc schema version" does not reference an existing slot.  New slot was created.
INFO:root:class "genome feature" slot "encodes" does not reference an existing slot.  New slot was created.
INFO:root:class "genome feature" slot "end" does not reference an existing slot.  New slot was created.
INFO:root:class "genome feature" slot "feature type" does not reference an existing slot.  New slot was created.
INFO:root:class "genome feature" slot "phase" does not reference an existing slot.  New slot was created.
INFO:root:class "genome feature" slot "seqid" does not reference an existing slot.  New slot was created.
INFO:root:class "genome feature" slot "start" does not reference an existing slot.  New slot was created.
INFO:root:class "genome feature" slot "strand" does not reference an existing slot.  New slot was created.
INFO:root:class "metabolite quantification" slot "highest similarity score" does not reference an existing slot.  New slot was created.
INFO:root:class "metabolite quantification" slot "metabolite quantified" does not reference an existing slot.  New slot was created.
INFO:root:class "metabolomics analysis activity" slot "has calibration" does not reference an existing slot.  New slot was created.
INFO:root:class "metabolomics analysis activity" slot "has metabolite quantifications" does not reference an existing slot.  New slot was created.
INFO:root:class "metaproteomics analysis activity" slot "has peptide quantifications" does not reference an existing slot.  New slot was created.
INFO:root:class "pathway" slot "has_part" does not reference an existing slot.  New slot was created.
INFO:root:class "peptide quantification" slot "all proteins" does not reference an existing slot.  New slot was created.
INFO:root:class "peptide quantification" slot "best protein" does not reference an existing slot.  New slot was created.
INFO:root:class "peptide quantification" slot "min_q_value" does not reference an existing slot.  New slot was created.
INFO:root:class "peptide quantification" slot "peptide sequence" does not reference an existing slot.  New slot was created.
INFO:root:class "peptide quantification" slot "peptide_spectral_count" does not reference an existing slot.  New slot was created.
INFO:root:class "peptide quantification" slot "peptide_sum_masic_abundance" does not reference an existing slot.  New slot was created.
INFO:root:class "protein quantification" slot "peptide_sequence_count" does not reference an existing slot.  New slot was created.
INFO:root:class "protein quantification" slot "protein_spectral_count" does not reference an existing slot.  New slot was created.
INFO:root:class "protein quantification" slot "protein_sum_masic_abundance" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction participant" slot "chemical" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction participant" slot "stoichiometry" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction" slot "direction" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction" slot "is balanced" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction" slot "is diastereoselective" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction" slot "is fully characterized" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction" slot "is stereo" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction" slot "is transport" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction" slot "left participants" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction" slot "right participants" does not reference an existing slot.  New slot was created.
INFO:root:class "reaction" slot "smarts string" does not reference an existing slot.  New slot was created.
INFO:root:class "read QC analysis activity" slot "input_read_bases" does not reference an existing slot.  New slot was created.
INFO:root:class "read QC analysis activity" slot "output_read_bases" does not reference an existing slot.  New slot was created.
INFO:root:class "study" slot "notes" does not reference an existing slot.  New slot was created.

INFO:root:Default_range not specified. Default set to 'string'

Unrecognized prefix: COG
Unrecognized prefix: EC
Unrecognized prefix: gtpo
Unrecognized prefix: insdc.srs
Unrecognized prefix: MetaCyc
Unrecognized prefix: MetaNetX
Unrecognized prefix: mgnify
Unrecognized prefix: rdfs
Unrecognized prefix: RetroRules
Unrecognized prefix: UniProtKB

WARNING:root:File "<file>", someline/somecol,  Prefix case mismatch - supplied: MIXS expected: mixs
WARNING:root:File "<file>", someline/somecol: Prefix case mismatch - supplied: MIXS expected: mixs

WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/FunctionalAnnotation
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/FunctionalAnnotationTerm
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/GenomeFeature
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/gff_coordinate
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/has_function
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/has_participants
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/OrthologyGroup
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/Pathway
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/Reaction
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/ReactionParticipant
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/annotation/subject
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/mixs/core_field
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/mixs/env_package
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/mixs/environment_field
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/mixs/investigation_field
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/mixs/nucleic_acid_sequence_source_field
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/mixs/sequencing_field
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/asm_score
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/binned_contig_num
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/contig_bp
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/contigs
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/ctg_L50
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/ctg_L90
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/ctg_logsum
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/ctg_max
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/ctg_N50
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/ctg_N90
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/ctg_powsum
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/gap_pct
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/gc_avg
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/gc_std
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/input_base_count
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/input_contig_num
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/input_read_count
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/lowDepth_contig_num
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/mags_list
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/MAGsAnalysisActivity
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/MetabolomicsAnalysisActivity
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/metagenome_assembly_parameter
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/MetagenomeAnnotationActivity
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/MetagenomeAssembly
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/MetaproteomicsAnalysisActivity
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/MetatranscriptomeActivity
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/MetatranscriptomeAnnotationActivity
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/MetatranscriptomeAssembly
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/NomAnalysisActivity
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/num_aligned_reads
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/num_input_reads
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/output_base_count
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/output_read_count
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/read_QC_analysis_statistic
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/ReadBasedAnalysisActivity
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/ReadQCAnalysisActivity
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_bp
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_L50
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_L90
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_l_gt50K
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_logsum
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_max
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_N50
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_N90
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_n_gt50K
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_pct_gt50K
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaf_powsum
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/scaffolds
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/too_short_contig_num
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/unbinned_contig_num
WARNING:root:No namespace defined for URI: https://microbiomedata/schema/workflow_execution_activity/WorkflowExecutionActivity

WARNING:root:Unrecognized prefix: biolink
WARNING:root:Unrecognized prefix: COG
WARNING:root:Unrecognized prefix: EC
WARNING:root:Unrecognized prefix: gtpo
WARNING:root:Unrecognized prefix: insdc.srs
WARNING:root:Unrecognized prefix: ISA
WARNING:root:Unrecognized prefix: MetaCyc
WARNING:root:Unrecognized prefix: MetaNetX
WARNING:root:Unrecognized prefix: mgnify
WARNING:root:Unrecognized prefix: rdfs
WARNING:root:Unrecognized prefix: RetroRules
WARNING:root:Unrecognized prefix: skos
WARNING:root:Unrecognized prefix: UniProtKB