pnrobinson
commented
8 years ago Thanks for this suggestion, which was in parallel to a related item. It is not possible to remove all of the brackets, because sometimes brakcets are simply part of the name of an item. However, we are endeavouring to remove brackets from all of the primary term names and to reduce their use as much as possible, so that neither primary names nor synonym names will use brackets to indicate alternatives.
Hi,
Using April 2016 hp.obo, I have found several term names and synonyms that contain abbreviations inside brackets. The brackets and abbreviations present an issue for text mining and NLP processing of these strings, so I propose to replace the strings containing abbreviations with two strings: a) a string without the abbreviation, and b) a string with the abbreviation. Below is a list of such terms with term id, an original string (either name or synonym), and recommended alternatives.
HP:0000654 Original: Decreased electroretinogram (ERG) amplitude Alternative 1: Decreased electroretinogram amplitude Alternative 2: Decreased ERG amplitude
HP:0011790 Original: Activating thyroid-stimulating hormone receptor (TSHR) defect Alternative 1: Activating thyroid-stimulating hormone receptor defect Alternative 2: Activating TSHR defect
HP:0003138 Original: Increased blood urea nitrogen (BUN) Alternative 1: Increased blood urea nitrogen Alternative 2: Increased BUN
HP:0000590 Original: External ophthalmoplegia, progressive (PEO) Alternative 1: External ophthalmoplegia, progressive Alternative 2: External PEO
HP:0003164 Original: Hypothalamic gonadotropin-releasing hormone (GNRH) deficiency Alternative 1: Hypothalamic gonadotropin-releasing hormone deficiency Alternative 2: Hypothalamic GNRH deficiency
HP:0011737 Original: Corticotropin-releasing hormone (CRH) deficient adrenal insufficiency Alternative 1: Corticotropin-releasing hormone deficient adrenal insufficiency Alternative 2: CRH deficient adrenal insufficiency
HP:0003402 Original: Decreased miniature endplate potentials (MEPP) Alternative 1: Decreased miniature endplate potentials Alternative 2: Decreased MEPP
HP:0000512 Original: Flattened or absent electroretinogram (ERG) Alternative 1: Flattened or absent electroretinogram Alternative 2: Flattened or absent ERG
HP:0003436 Original: Prolonged miniature endplate potentials (MEPP) Alternative 1: Prolonged miniature endplate potentials Alternative 2: Prolonged MEPP
HP:0011789 Original: Thyroid-stimulating hormone receptor (TSHR) defect Alternative 1: Thyroid-stimulating hormone receptor defect Alternative 2: TSHR defect
HP:0011791 Original: Inactivating thyroid-stimulating hormone receptor (TSHR) defect Alternative 1: Inactivating thyroid-stimulating hormone receptor defect Alternative 2: Inactivating TSHR defect
HP:0003760 Original: Percussion-induced rapid rolling muscle contractions (PIRC) Alternative 1: Percussion-induced rapid rolling muscle contractions Alternative 2: PIRC
HP:0000512 Original: Abnormal electroretinogram (ERG) Alternative 1: Abnormal electroretinogram Alternative 2: Abnormal ERG
HP:0011735 Original: Adrenocorticotropin (ACTH) deficient adrenal insufficiency Alternative 1: Adrenocorticotropin deficient adrenal insufficiency Alternative 2: ACTH deficient adrenal insufficiency
HP:0003785 Original: Decreased CSF homovanillic acid (HVA) Alternative 1: Decreased CSF homovanillic acid Alternative 2: Decreased CSF HVA
HP:0003431 Original: Decreased motor nerve conduction velocity (NCV) Alternative 1: Decreased motor nerve conduction velocity Alternative 2: Decreased motor NCV
HP:0003431 Original: Decreased motor nerve conduction velocities (NCV) Alternative 1: Decreased motor nerve conduction velocities Alternative 2: Decreased motor NCV
HP:0007984 Original: Reduced rod b-wave (ERG) Alternative 1: Reduced rod b-wave Alternative 2: Reduced rod ERG
HP:0003657 Original: Granular osmiophilic deposits (GROD) in cells Alternative 1: Granular osmiophilic deposits in cells Alternative 2: GROD in cells
HP:0008259 Original: Adrenocorticotropin (ACTH) receptor (ACTHR) defect Alternative 1: Adrenocorticotropin receptor defect Alternative 2: ACTH receptor defect Alternative 3: ACTHR defect
HP:0001511 Original: Intrauterine growth retardation (IUGR) Alternative 1: Intrauterine growth retardation Alternative 2: IUGR
HP:0001491 Original: Congenital fibrosis of extraocular muscles (CFEOM) Alternative 1: Congenital fibrosis of extraocular muscles Alternative 2: CFEOM
HP:0005978 Original: Noninsulin dependent diabetes mellitus (NIDDM) Alternative 1: Noninsulin dependent diabetes mellitus Alternative 2: NIDDM
HP:0000654 Original: Reduced electroretinogram (ERG) Alternative 1: Reduced electroretinogram Alternative 2: Reduced ERG
HP:0001312 Original: Giant somatosensory evoked potentials (SEPS) Alternative 1: Giant somatosensory evoked potentials Alternative 2: Giant SEPS
HP:0003448 Original: Decreased sensory nerve conduction velocities (NCV) Alternative 1: Decreased sensory nerve conduction velocities Alternative 2: Decreased sensory NCV
HP:0011738 Original: Corticotropin-releasing hormone receptor (CRHR) defect Alternative 1: Corticotropin-releasing hormone receptor defect Alternative 2: CRHR defect
HP:0011945 Original: Bronchiolitis obliterans organizing pneumonia (BOOP) Alternative 1: Bronchiolitis obliterans organizing pneumonia Alternative 2: BOOP
HP:0007385 Original: aplasia cutis congenita (ACC) Alternative 1: aplasia cutis congenita Alternative 2: ACC
HP:0007984 Original: Reduced amplitude of b-wave (ERG) Alternative 1: Reduced amplitude of b-wave Alternative 2: Reduced amplitude of ERG
HP:0002494 Original: Abnormal rapid eye movement (REM) sleep Alternative 1: Abnormal rapid eye movement sleep Alternative 2: Abnormal REM sleep
HP:0003236 Original: Increased creatine phosphokinase (CPK) Alternative 1: Increased creatine phosphokinase Alternative 2: Increased CPK
HP:0003288 Original: Mitochondrial propionyl-CoA carboxylase (PCC) defect Alternative 1: Mitochondrial propionyl-CoA carboxylase defect Alternative 2: Mitochondrial PCC defect
HP:0006548 Original: Pulmonary arteriovenous malformation (PAVM), especially lower lobes Alternative 1: Pulmonary arteriovenous malformation, especially lower lobes Alternative 2: PAVM, especially lower lobes
HP:0003240 Original: Increased phosphoribosylpyrophosphate (PRPP) synthetase Alternative 1: Increased phosphoribosylpyrophosphate synthetase Alternative 2: Increased PRPP synthetase
HP:0001631 Original: Atrial septal defect (ASD) Alternative 1: Atrial septal defect Alternative 2: ASD
HP:0007688 Original: Absent cone and rod functions by electroretinogram (ERG) Alternative 1: Absent cone and rod functions by electroretinogram Alternative 2: Absent cone and rod functions by ERG
HP:0002928 Original: Decreased activity of the pyruvate dehydrogenase (PDH) complex Alternative 1: Decreased activity of the pyruvate dehydrogenase complex Alternative 2: Decreased activity of the PDH complex
HP:0003165 Original: Elevated circulating parathyroid hormone (PTH) level Alternative 1: Elevated circulating parathyroid hormone level Alternative 2: Elevated circulating PTH level
HP:0011738 Original: Corticotropin-releasing hormone receptor (CRHR) resistance Alternative 1: Corticotropin-releasing hormone receptor resistance Alternative 2: CRHR resistance
HP:0003436 Original: Prolonged miniature endplate currents (MEPC) Alternative 1: Prolonged miniature endplate currents Alternative 2: Prolonged MEPC
HP:0003145 Original: Decreased adenosylcobalamin (ADOCBL) Alternative 1: Decreased adenosylcobalamin Alternative 2: Decreased ADOCBL
HP:0000762 Original: Decreased nerve conduction velocities (NCV) Alternative 1: Decreased nerve conduction velocities Alternative 2: Decreased NCV
HP:0003203 Original: Negative nitroblue tetrazolium (NBT) reduction test Alternative 1: Negative nitroblue tetrazolium reduction test Alternative 2: Negative NBT reduction test
HP:0002959 Original: Impaired Ig class-switch recombination (CSR) Alternative 1: Impaired Ig class-switch recombination Alternative 2: Impaired Ig CSR