GeneCup: Mining Gene Relationships from Pubmed using Custom Ontology

Custom Ontology Editor

The custom ontology has four layers. The top layer is one single keyword serves as the name of the ontology. This keyword is used to select the ontology used for each search (i.e. via the dropdown menu). A new ontology will be created if the ontology does not already exist for the use. Keywords in the second layer describe the main concepts and are used to include/exclude groups of keywords for each search (via check boxes). All keywords under the same second layer are shown with the same color in the graphic output. Keywords in the third layer are shown in the results (both graphic and tabular). Keywords in the fourth layer are used in PubMed and GWAS catalog search. These keywords will also be highlighted in the sentences. Results from all keywords in the fourth layer are grouped together and shown under their parent third layer keyword. This is useful to include synonyms and spelling variants in the fourth layer. A special second layer keyword is GWAS. Any keyword under this branch is used to search the GWAS catalog. Similarly, third layer is used for display of the results and fourth layer is used for search.

The ontologies will be saved after login. Custom ontologies are available after login.

Add or remove keywords from the addiction ontology

Layer 1. Name of the ontology (e.g. addiction)

Layer 2. Main category (e.g. brain region )

Layer 3. A keyword displayed in the results (e.g. accumbens)

Layer 4. Keywords used for the search (Please include the word in Layer 3 and its variations, such as synonyms or alternative spellings, e.g. accumbens, accumbal, AcbC, AcbS, NAcc )

Ontology: addiction

brain
- accumbens
  - acbc, acbs, accumbal, accumbens, core, Nacc, NacSh, shell
- amygdala
  - amy, amygdala, bla, cea, cna
- cortex
  - cerebral, cingulate, cortex, cortico limbic, corticolimbic, corticostriatal, infralimbic, insular, mPFC, orbitofrontal, pfc, prefrontal, prelimbic, prl, vmpfc
- habenula
  - habenula, lhb, mhb
- hippocampus
  - ca1, ca3, dentate gyrus, dhpc, hip, hipp, hippocampal, hippocampus, subiculum, vhipp, vhpc
- hypothalamus
  - hypothalamic, hypothalamus, LHA, paraventricular nucleus, PVN
- striatum
  - basal ganglia, caudate, globus pallidus, GPI, putamen, STR, striatal, striatum
- VTA
  - limbic, mesoaccumbal, mesoaccumbens, mesolimbic, midbrain, pvta, ventral tegmental, vta

addiction
- addiction
  - addiction, addictive, compulsive, drug abuse, escalation, punishment
- aversion
  - aversion, aversive, conditioned taste aversion, CTA
- dependence
  - dependence
- intoxication
  - binge, intoxication
- relapse
  - craving, drug seeking, reinstatement, relapse, seeking
- reward
  - conditioned place preference, CPP, drug reinforced, hedonic, ICSS, incentive, instrumental response, intracranial self stimulation, operant, reinforcement, reinforcing, reward, self administered, self administration
- sensitization
  - behavioral sensitization, locomotor sensitization, drug sensitization, incentive sensitization
- social
  - social
- withdrawal
  - withdrawal

drug
- alcohol
  - acamprosate, alcohol, alcoholics, alcoholism, antabuse, campral, disulfiram, ethanol, naltrexone, revia, vivitrol
- amphetamine
  - AMPH, amphetamine, METH, methamphetamine
- benzodiazepine
  - adinazolam, alprazolam, benzodiazepine, benzos, brotizolam, chlordiazepoxide, climazolam, clobazam, clonazepam, clorazepate, diazepam, estazolam, flunitrazepam, flurazepam, halazepam, librium, loprazolam, lorazepam, lormetazepam, midazolam, nimetazepam, nitrazepam, normison, oxazepam, prazepam, temazepam, triazolam, valium, xanax
- cannabinoid
  - acylethanolamines, cannabichromene, cannabidiol, cannabigerol, cannabinoids, cannabinol, cannabis, cannabivarin, cesamet, drobinal, dronabinol, endocannabinoids, epidiolex, JWH 018, JWH 122, JWH 250, marijuana, marinol, nabilone, Oleoylethanolamide, palmitoylethanolamide, phytocannabinoid, rimonabant, SR141716, SR144528, syndros, tetrahydrocannabinol, tetrahydrocannabivarin, thc, thc 9
- cocaine
  - cocaine
- nicotine
  - nicotine, smokers, smoking, tobacco
- opioid
  - buprenorphine, codeine, fentanyl, heroin, hycodan, hydrocodone, hydromorphone, kadian, kratom, methadone, morphine, naloxone, opioids, oxycodone, oxycontin, percocet, suboxone, tramadol, ultram, vicodin
- psychedelics
  - ayahuasca, ecstasy, ibogaine, ketamine, LSD, lysergic acid diethylamide, MDMA, mescaline, methylenedioxymethamphetamine, N methoxybenzyl, NBOMes, peyote, psilocybin, psychedelic, psychedelics

function
- neuroplasticity
  - boutons, epsc, epsp, IPSC, IPSP, long term depression, long term potentiation, LTD, LTP, mIPSC, neurite, neurogenesis, neuroplasticity, plasticity, synaptic
- neurotransmission
  - 5 ht, acetylcholine, cholinergic, DAergic, dopamine, dopaminergic, GABA, GABAergic, glutamate, glutamatergic, muscarinic, neuropeptides, neurotransmission, nicotinic, serotonergic, serotonin
- signalling
  - glycosylation, phosphorylation, signaling, signalling, kinase, binding, signal transduction, second messengers, cGMP, cAMP
- transcription
  - histone, hypermethylation, hypomethylation, methylation, ribosome, transcription

psychiatric
- anxiety
  - anxiety, anxious
- autism
  - autism, autistic
- bipolar
  - bipolar disorder
- compulsive
  - compulsive, obsessive
- depression
  - depression, depressive, major depressive disorder, MDD
- impulsivity
  - 5 CSRTT, 5 choice task, delay discounting, delay exposure, delay intolerance, delayed reward, delay task, five choice serial reaction time task, impulsive, impulsivity, premature responding
- schizophrenia
  - schizophrenia

cell
- neuron
  - adrenergic neurons, cholinergic neurons, dopaminergic neurons, gabaergic neurons, glutamatergic neurons, GnRH neurons, interneurons, monoaminergic neurons, medium spiny neurons, motor neurons, neuronal cells, nitrergic neurons, noradrenergic neurons, projection neurons, pyramidal neurons, sensory neurons, serotonergic neurons, somatostatin neurons, neurons, excitatory neurons, inhibitory neurons, corticospinal neurons, dopamine neurons, D1 neurons, D2 neurons, afferent neurons, efferent neurons, serotonin neurons, cortical neurons, hippocampal neurons, DA neurons, CNS neurons, cortex neurons, mesencephalic neurons, orexin neurons, catecholaminergic neurons, striatal neurons, bipolar neurons, ganglion cells, RGC, horizontal cells, amacrine cells
- astrocyte
  - astrocytic, astrocytes, astroglia, astroglial
- microglia
  - microglia, microglial
- endothelium
  - endothelium, endothelial cells
- oligodendrocyte
  - oligodendrocytes

stress
- PTSD
  - PTSD, post traumatic stress, post traumatic stress symptoms, post traumatic stress disorder
- stress
  - distress, psychological trauma, stress

GWAS
- psychiatric
  - psychiatric, schizophrenia, autism, depression, anxiety, bipolar, mental
- nicotine
  - nicotine, smoking, chronic obstructive, tobacco
- addiction
  - addiction, cocaine, opioid, morphine, amphetamine, methadone, heroin, drug dependence
- alcohol
  - alcohol