<commit_before># from so_defs file

AntisensePrimaryTranscript=The reverse complement of the primary transcript.
AntisenseRNA=Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
ARS=A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
Assembly=A sequence of nucleotides  that has been algorithmically derived from an alignment of two or more different sequences.
AssemblyComponent=A region of sequence which may be used to manufacture a longer assembled, sequence. 
Attenuator=A sequence segment located between the promoter and a structural gene that causes partial termination of transcription.
AutocatalyticallySplicedIntron=A self spliced intron.
BindingSite=A region on the surface of a molecule that may interact with another molecule.
BranchSite=A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
Cap=A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
CDNAMatch=A match against cDNA sequence.
CDS=A contiguous RNA sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
Centromere=A region of chromosome where the spindle fibres attach during mitosis and meiosis.
ChromosomalDeletion=An incomplete chromosome.
Chromosome=Structural unit composed of long DNA molecule. 
Clip=Part of the primary transcript that is clipped off during processing.
Clone=A piece of DNA that has been inserted in a vector so that it can be propagated in E. coli or some other organism.
CloneEnd=The end of the clone insert.
CloneStart=The start of the clone insert.
Codon=A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together signify a unique amino acid or the termination of translation. 
ComplexSubstitution=When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.
Contig=A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unknown/unavailable bases.
CpGIsland=Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
CRM=A regulatory region where more than 1 transcription factor binding site together are regulatorily active.
CrossGenomeMatch=A nucleotide match against a sequence from another organism.
DatabankEntry=The sequence referred to by an entry in a databank such as GenBank or UniProt.
DecayedExon=A non-functional descendent of an exon.
Deletion=The sequence that is deleted.
DeletionJunction=The space between two bases in a sequence which marks the position where a deletion has occurred.
DirectRepeat=A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.
DispersedRepeat=A repeat that is located at dispersed sites in the genome.
Enhancer=A cis-acting sequence that increases the utilisation of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
EnzymaticRNA=A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
EST=Expressed Sequence Tag: The sequence of a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
ESTMatch=A match against an EST sequence.
Exon=A region of the genome that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205).
ExonJunction=The boundary between two exons in a processed transcript.
ExperimentalResultRegion=A region of sequence implicated in an experimental result.
ExpressedSequenceMatch=A match to an EST or cDNA sequence.
FivePrimeUTR=A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
FlankingRegion=The DNA sequences extending on either side of a specific locus.
Gene="Gene" is an abstract term used to describe a collection of transcripts and related regulatory features.
GeneGroup=A collection of related genes.
GenePart=A part of a gene.
GoldenPath=A set of subregions selected from sequence contigs which when concatenated form a non-redundant linear sequence.
GoldenPathFragment=One of the pieces of sequence that make up a golden path.
GroupIIIntron=Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
GroupIIntron=Group I catalytic introns are large self-splicing ribozymes. They catalyse their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.
GuideRNA=short 3'-uridylated RNA that can form a perfect duplex (except for the oligoU tail (SO:0000609)) with a stretch of mature edited mRNA.
HammerheadRibozyme=A small catalytic RNA motif that catalyses self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs. 
Insertion=A region of sequence identified as having been inserted.
InsertionSite=The site where an insertion occurred.
IntegratedVirus=A viral sequence which has integrated into the host genome.
IntergenicRegion=The region between two known genes.
Intron=A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
Inversion=A continuous nucleotide sequence is inverted in the same position.
InvertedRepeat=The sequence is complementarily repeated on  the opposite strand. Example: GCTGA-----TCAGC.
Junction=A junction refers to an interbase location of zero in a sequence.
LocatedSequenceFeature=A biological feature that can be attributed to a region of biological sequence.
Match=A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
MatchPart=A part of a match, for example an HSP from BLAST isa match_part.
MatchSet=A collection of match parts
MaturePeptide=The coding sequence for the mature or final peptide or protein product following post-translational modification.
MethylatedA=A methylated adenine.
MethylatedBaseFeature=A nucleotide modified by methylation.
MethylatedC=A methylated deoxy-cytosine.
Microsatellite=A very short unit sequence of DNA (2 to 4 bp) that is repeated multiple times in tandem.
Minisatellite=A repetitive sequence spanning 500 to 20,000 base pairs (a repeat unit is 5 - 30 base pairs).
MiRNA=Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. miRNAs are produced from precursor molecules (SO:0000647) that can form  local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA  molecule accumulates from one arm of a hairpin-precursor molecule. miRNAs  may trigger the cleavage of their target molecules or act as translational repressors.
ModifiedBaseSite=A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U.
MRNA=The intermediate molecule between DNA and protein.
NcRNA=An mRNA sequence that does not encode for a protein rather the RNA molecule is the gene product.
NcPrimaryTranscript=A primary transcript that is never translated into a protein.
NucleaseSensitiveSite=A region of nucleotide sequence targeting by a nuclease enzyme.
NucleotideMatch=A match against a nucleotide sequence.
NucleotideMotif=A region of nucleotide sequence  corresponding to a known motif.
Oligo=A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
Operon=A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
ORF=A nucleic acid sequence that, when read as sequential triplets, has the potential of encoding a sequential string of amino acids.
OriginOfReplication=The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
PCRProduct=A region amplified by a PCR reaction.
PointMutation=A mutation event where a single DNA nucleotide changes into another nucleotide.
PolyASequence=Sequence of about 100 nucleotides of A at the 3' end of most eukaryotic mRNAs.
PolyASignalSequence=The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
PolyASite=The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation.
Polypeptide=A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
PolypeptideDomain=A region of a single polypeptide chain  that folds into an independent unit and exhibits biological activity. A  polypeptide chain may have multiple domains.
PolypyrimidineTract=The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
PossibleAssemblyError=A region of sequence where there may have been an error in the assembly.
PossibleBaseCallError=A region of sequence where the validity of the base calling is questionable.
PrecursorMiRNA=A miRNA transcript that has not been diced.
PrecursorRasiRNA=A rasiRNA transcript that has not been diced.
PrecursorSiRNA=A siRNA transcript that has not been diced.
PrimaryTranscript=The primary (initial, unprocessed) transcript; includes five_prime_clip (SO:0000555), five_prime_untranslated_region (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188) and three_prime_ untranslated_region (three_prime_UTR), and three_prime_clip (SO:0000557).
Primer=A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase.
ProbeSet=A set of probes which can be mapped to Genes.  For example, the Affymetrix Drosophila genome 2.0 array set.
ProcessedTranscript=A transcript which has undergone processing. The processing may include intron removal, 5' capping and polyadenlyation.
Promoter=The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
ProteinCodingPrimaryTranscript=A primary transcript that, at least in part, encodes one or more proteins.
ProteinMatch=A match against a protein sequence.
Pseudogene=A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). On occasion a pseudogene is functional as a consequence being "captured" by a non-paralogous gene, it is then known as a "captured_pseudogene" (SO:0100042). definition_reference:
PseudogenicRegion=A non-functional descendent of a functional entity.
RasiRNA=A small, 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
Read=A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
ReadPair=A pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
Reagent=A sequence used in experiment.
Region=Contiguous sequence.
RegulatoryRegion=A DNA sequence that controls the expression of a gene.
Regulon=A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.
Remark=A comment about the sequence.
RepeatFamily=A group of characterised repeat sequences.
RepeatRegion=A region of sequence containing one or more repeat sequences.
RestrictionEnzymeCutSite=A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA. 
RestrictionFragment=Any of the individual polynucleotide sequences produced by digestion of DNA with a restriction endonuclease.
RFLPFragment=A  polymorphism detectable by the size differences in DNA fragments generated by a restriction enzyme.
RibosomeEntrySite=Region in 5' UTR where ribosome assembles on mRNA.
Ribozyme=An RNA with catalytic activity.
RNAiReagent=A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
RNAiResult=The result from an RNAi screen. 
RNaseMRPRNA=The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
RNasePRNA=The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5 prime  ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
RRNA=RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
RRNA18S=18S_rRNA -A large polynucleotide which functions as a part of the small subunit of the ribosome
RRNA28S=A component of the large ribosomal subunit.
RRNA58S=5.8S ribosomal RNA (5.8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5.8S rRNA is also found in archaea.
RRNA5S=5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilises 5S rRNA until it is required for transcription.
SAGETag=A short diagnostic sequence tag,  serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
ScRNA=Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote. 
SequenceDifference=A region where the sequences differs from that of a specified sequence.
SequenceVariant=A region of sequence where variation has been observed.
SignalPeptide=The sequence  for an N-terminal domain of a secreted protein; this domain is involved in  attaching nascent polypeptide to the membrane leader sequence.
Silencer=Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes.
SiRNA=Small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. sRNAs trigger the cleavage of their target molecules.
SmallRegulatoryNcRNA=A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
SnoRNA=Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed, the box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localisation, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.
SNP=SNPs are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist in normal individuals in some population(s), wherein the least frequent allele has an abundance of 1% or greater.   
SnRNA=Small non-coding RNA in the nucleoplasm.
SpliceosomalIntron=An intron which is spliced by the spliceosome.
SpliceAcceptor=The junction between the 3 prime end of an intron and the following exon.
SpliceDonor=The junction between the 3 prime end of an exon and the following intron.
SpliceEnhancer=Region of a transcript that regulates splicing.
SpliceSite=The position where intron is excised.
SRPRNA=The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilises helix 8 for SRP54 binding.
StRNA=Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in  C. elegans.
STS=Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
Substitution=Any change in genomic DNA caused by a single event.
Supercontig=One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
SyntenicRegion=A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.
Tag=A nucleotide sequence that may be used to identify a  larger sequence.
TandemRepeat=Two or more adjacent copies of a DNA sequence.
TelomeraseRNA=The RNA component of telomerase, a reverse transcriptase that synthesises telomeric DNA.
Telomere=A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end,
Terminator=The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
TFBindingSite=A region of a molecule that binds to a transcription factor.
TFmodule=A regulatory region where more than 1 transcription factor binding site together are regulatorily active.
ThreePrimeUTR=A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
TilingPath=A set of regions which overlap with minimal polymorphism to form a linear sequence.
TilingPathFragment=A piece of sequence that makes up a tiling_path (SO:0000472.).
TmRNA=tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. tmRNAs have been identified in eubacteria and some chloroplasts but are absent from archaeal and eukaryote nuclear genomes.
Transcript=An RNA synthesised on a DNA or RNA template by an RNA polymerase.
TranscriptionEndSite=The region where transcription ends.
TranscriptionStartSite=The region where transcription begins.
TranslatedNucleotideMatch= A match against a translated sequence.
TransposableElement=A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
TransposableElementGene=A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
TransposableElementInsertionSite=The site in a genome where a transposable_element has inserted.
TransSpliceAcceptorSite=The process that produces mature transcripts by combining exons of independent pre-mRNA molecules. The acceptor site lies on the 3' of these molecules
TRNA=Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. tRNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). tRNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
U11SnRNA=U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
U12SnRNA=The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
U14SnRNA=U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
U1SnRNA=U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
U2SnRNA=U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
U4atacSnRNA=An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
U4SnRNA=U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to re-fold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
U5SnRNA=U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
U6atacSnRNA=U6atac_snRNA -An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
U6SnRNA=U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
UTR=Messenger RNA sequences that are untranslated and lie five prime and three prime to sequences which are translated.
VaultRNA=A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
VirtualSequence=A continuous piece of sequence similar to the 'virtual contig' concept of Ensembl.
YRNA=Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.



# Additional FlyMine-specific definitions
AGambiaeLifeCycle=Result from an Anopheles gambiae microarray experiment.
Amplicon=A piece of DNA that has been synthesised using amplification techniques.
Analysis=The description of a computational algorithm or experimental procedure.
AnalysisResult=The result of a computational algorithm or an experimental procedure that provides evidence for the existence of a piece of data.
AnatomyTerm=A structured controlled vocabulary term of the anatomy of Drosophila melanogaster, used, for example, for the description of phenotypes and where a gene is expressed.
Annotation=Links the BioProperties of BioEntities with the evidence for that BioProperty.
ArtificialDeletion=A nucleic acid sequence that is deleted artificially in the genome as opposed to being deleted naturally.
Author=The author of a publication.
BAC=Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host
BioEntity=The BioEntity class is the parent for more specialised classes of biological entities, such as Gene, Transcript etc.
BioProperty=Biological properties that have been assigned to BioEntities, such as GO annotation and phenotypes.
BlastMatch=A region of sequence, aligned to another sequence with some statistical significance, using the BLAST algorithm.
CDNAClone=Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
ChromosomeArm=A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere
ChromosomeBand=A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
Chunk=In order to provide access to the sequence of Anopheles gambiae and to facilitate annotation, scaffolds are treated as 'clones' in the Ensembl databases, and the larger scaffolds have been divided into chunks of approximately 25 kb.
Comment=A comment or description about a biological object (BioEntity).
CompositeSequence=A set of reporters used collectively to measure an expression of a particular gene, exon, or splice-variant.
ComputationalAnalysis=The description of a computational algorithm.
ComputationalResult=The result of a computational algorithm.
Database=An external database.
DataSet=A set of results or data from a data source.
DataSource=The origin of imported data.
Disease=Objects of this class are contain disease descriptions from the <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM">OMIM database</a>
ESTCluster= Set of joined ESTs.
Evidence=Provides evidence for a Relation, BioEntity or Annotation. The evidence could be a publication, external database or experimental or computational result.
Experiment=The description of an experimental procedure.
ExperimentalResult=The result of an experimental procedure.
FlyAtlasResult=A result from the FlyAtlas microarray project.
ForwardPrimer=A single stranded oligo used for polymerase chain reaction.
GenomeRegion=Continuous genomic sequence.
GOAnnotation=Objects of class GOAnnotation hold the Gene Ontology annotation for a gene.
GOEvidence=An evidence assigned by a GO annotator.
GOEvidenceCode=A three-letter code that indicates how annotation to a particular GO term is supported. These evidence codes correspond to broad categories of experimental or other support. 
GOTerm=A term from the Gene Ontology.
Group=Chromosome groups of Apis mellifera were assembled by joining scaffolds.
Homologue=Gene with common ancestry. A homologue can be an orthologue (genes separated by the event of speciation) or paralogue (genes separated by the event of genetic duplication).
InfoSource=The source of published information, either a publication or an external database.
InterMineObject=The parent class of all other classes in the database.
InterproEvidence=Extra evidence for InterPro objects.
Location=The location of one BioEntity on another.
Marker=A short sequence whose placement on the genome is known.
MicroArrayAssay=A single assay of a microarray experiment involving samples at particular conditions against a particular microarray chip. 
MicroArrayExperiment=A microarray experiment comprising multiple assays.
MicroarrayOligo=A gene-specific oligonucleotide designed for use in a microarray experiment.
MicroArrayResult=Numerical result for one sequence/sample pair in a particular microarray assay or derived from multiple assays.
ModelledProteinStructure=The three-dimensional conformation of a protein, as predicted by computational analysis.
Motif=A sequence motif is a short region of biological interest.
NuclearDNA=DNA that can be found in the nucleus of a cell.
Ontology=A controlled vocabulary.
OntologyRelation=The relationship between two terms in an ontology.
OntologyTerm=A term within an ontology.
OntologyTermSynonym=A synonym for a term from an ontology - an alternative name or symbol for a term.
Organism=A living thing.
Orthologue=Orthologues are equivalent genes in different species that evolved from a common ancestor by speciation.
OverlapRelation=Description of a pair of genome annotation features that have overlapping locations on a chromosome.
Paralogue=Paralogues are genes from the same homologous super-family found in another part of the genome of a particular taxon. Paralogues are the result of gene duplication.
PartialLocation=The location of part of a BioEntity on another.
Pathway=Molecular interaction network.
Phenotype=The observable characteristics of an organism. The expression of gene alleles (genotype) as an observable physical or biochemical trait.
Protein=One or more polypeptides which may, or may not, be covalently bonded, and which assume a native secondary and tertiary structure.
ProteinBindingSite=A region of a molecule that binds to a protein.
ProteinDomain=A region of a protein that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
ProteinFamily=A group of characterised protein sequences.
ProteinInteraction=A relation between two proteins which have been shown to be related through a physical interaction.
ProteinInteractionExperiment=The description of a particular protein interaction experiment.
ProteinInteractionRegion= The region of a protein molecule that binds to another protein molecule.
ProteinInteractionTerm=A term from the PSI-MI protein interaction ontology.
ProteinInteractor=A term for a protein involved in a protein interaction.
ProteinRegion=Amino acid sequence of part of a protein.
ProteinStructure=The three-dimensional conformation of a protein.
ProteinStructureExperiment=The type of experiment that was done to determine a protein structure.
Protocol=Documentation of the set of steps taken in a procedure.
Publication=A journal article, book etc.
RankedRelation=A relation that is part of an ordered set of relations. eg. the relationship between transcripts and exons.
Relation=Any relationship between two BioEntities. A relation object has a subject BioEntity and an object BioEntity.
Reporter=The nucleotide sequence present in a particular location on the array
ReversePrimer=A single stranded oligo used for polymerase chain reaction.
RNAiExperiment=The description of a particular RNAi experiment.
RNAiPhenotype=the phenotype of an RNA interference experiment.
RNAiResult=The result from an RNAi screen. This can be either a defined phenotype as a result from an in vivo screen (RNAiPhenotype) or a result from a screen done in cell culture (RNAiScreenHit).
RNAiScreen=A large-scale RNA interference experiment.
RNAiScreenHit=One experimental result from an RNAi screen (not necessarily a defined phenotype). Currently this is a result from one of the D. melanogaster RNAi screens done in cell-culture.
Sample=Description of the source of biological material. Can include information on such properties as species, developmental stage, organism part, gender and cell type.
SampleCharacteristic=Description of some characteristic (type and value) of a sample.
Scaffold=Larger sequence contigs that result from the assembly of shorter (often whole genome shotgun, WGS) sequencing reads which could not yet be assembled into chromosomes. Generally, more genome sequencing, narrowing of gaps and establishment of a tiling path is necessary before a chromosome assembly can be established.
Sequence=The order of building blocks in biological macromolecules like DNA, RNA, protein and polysaccharides.
SimpleRelation=A simple relationship between two BioEntities.
SymmetricalRelation=A relationship between two BioEntities that doesn't have direction - all objects are related to each other in the same way.
Synonym=Another name by which a BioEntity is known.
TilingPathSpan=A tiling path is a set of regions which overlap with minimal polymorphism to form a linear sequence. A TilingPathSpan starts at the initiation codon of one gene and ends at the initiation codon of a neighbouring gene or at a transposable element.
TiffinExpressionTerm=Expression term to which a Tiffin motif is associated. Motifs were assigned an expression term from the <a href="http://www.fruitfly.org/cgi-bin/ex/go.cgi">ImaGO controlled vocabulary</a> according to the <a href="http://www.fruitfly.org/cgi-bin/ex/insitu.pl">in-situ expression pattern</a> of nearby genes.
Translation=A possible translation of (part of) a gene that differs from the amino acid sequence found in the corresponding wild-type protein.
Treatment=A treatment is the process or action applied to a particular sample.
TreatmentParameter=A variable within the treatment.
UniProtFeature=A region or site of interest in a protein sequence (source: UniProt). Examples: post-translational modifications, binding sites, enzyme active sites, local secondary structures.
Vector=A DNA molecule that can be used to transfer DNA molecules between organisms.






# Class field descriptions

Gene.identifier=Any identifier, other than the main organism genome database identifier, which \
is commonly used to identify a gene (for example, the Drosophila CG identifier). See 'Synonyms' \
for other gene names and identifiers for this gene.<p>\

Gene.primaryIdentifier=The main identifier used by the organisms main genome database. \
For example, the FBgn identifier assigned by FlyBase or the WBGene identifier assigned by WormBase. \
See 'Synonyms' for other gene names and identifiers for this gene.<p>\

Gene.name=The gene symbol or common name. For most organisms this will be an officially assigned \
symbol/name (for example, the FlyBase gene symbol or the CGC-approved gene name for C. elegans). \
See 'Synonyms' for other gene names and identifiers for this gene.<p>\

Protein.primaryAccession=UniProt primary accession. See 'Synonyms' for other names and identifiers \
for this protein.
Protein.identifier=UniProt entry name (for example 18C_DROME). See 'Synonyms' for other names and \
identifiers for this protein.

Gene.allGoAnnotation=For a particular GO term, this provides that GO term and all the parent terms for that GO term.

Gene.length=Genomic length of the gene, i.e. sequences of all introns and exons.

Homologue.type=A homologue can be either an orthologue (related to the gene by the event of speciation and likely to be functionally related) or an inparalogue (related to the gene by a duplication event after a speciation of interest).

Homologue.inParanoidScore=The inparanoid program calculates orthologue \
and inparalogue clusters, pairwise between two organisms, by first \
finding the best recipricol blast match for each gene. This becomes \
the seed-orthologue to which inparalogues are clustered. Each member \
in the cluster receives an inparalog score which reflects the distance \ 
to the seed-orthologue. A score of 1.0 means there is identical \
distance to the seed orthologue (and so all orthologues in the cluster \
will have an inparanoid score of 1.0). Each inparalogue in the cluster \
will have a score less than one which reflects how similar it is to \
the seed orthologue.

Homologue.bootstrapScore=the confidence that this ortholog pair \
are true orthologues. (This is estimated by sampling how often the \
pair is found as recipricolly best matches by a bootstrapping \
procedure applied to the original Blast alignment).

Homologue.homologueBootstrapScore=the confidence that this ortholog pair \
are true orthologues. (This is estimated by sampling how often the \
pair is found as recipricolly best matches by a bootstrapping \
procedure applied to the original Blast alignment).

Homologue.clusterName=The inparanoid program calculates orthologue and \
inparalogue clusters, pairwise between two organisms, by first finding \
the best recipricol blast match for each gene. This becomes the \
seed-orthologue to which inparalogues are clustered. Each cluster can be identified by a unique cluster name.

FlyAtlasResult.affyCall=Reflects an up- or down-regulation (or no change at all) compared to the whole fly.

FlyAtlasResult.enrichment=This factor tells you how much higher the signal is in a particular tissue than in the whole fly, i.e. whether the gene is tissue-specific. 

FlyAtlasResult.MRNASignal=Abundance of the mRNA. FlyAtlas considers values over 100 as being abundant, and anything over 1000 as remarkable.

FlyAtlasResult.MRNASignalSEM= The SEM value tells you how consistent or variable the MRNASignal is.

FlyAtlasResult.presentCall=How many of the four arrays for each sample actually gave a detectable expression, according to Affymetrix's GCOS software. 

RNAiScreenHit.maxOffTargetOverlaps=The maximum continuous sequence overlap of potential off-target(s).

RNAiScreenHit.numOffTargets=The number of potential off-targets based on sequence matches: at least one length of 19 bp or more with matching sequence of 19 bp or more of this amplicon.

GOAnnotation.evidenceCode=Every GO annotation must indicate the type of evidence that supports it. \
The possibilities are:<p>\
<table>\
 <tr> <td>IC:</td><td> Inferred by Curator</td>              <td>&nbsp;</td> <td>IDA:</td> <td> Inferred from Direct Assay </td> </tr>\
 <tr> <td>IEA:</td><td> Inferred from Electronic Annotation</td>      <td>&nbsp;</td> <td>IEP:</td> <td> Inferred from Expression Pattern</td> </tr>\
 <tr> <td>IGI:</td><td> Inferred from Genetic Interaction</td>       <td>&nbsp;</td> <td>IMP:</td> <td> Inferred from Mutant Phenotype</td> </tr>\
 <tr> <td>IPI:</td><td> Inferred from Physical Interaction</td>      <td>&nbsp;</td> <td>ISS:</td> <td> Inferred from Sequence or Structural Similarity</td> </tr>\
 <tr> <td>NAS:</td><td> Non-traceable Author Statement</td>        <td>&nbsp;</td> <td>ND:</td> <td> No biological Data available</td> </tr>\
 <tr> <td>RCA:</td><td> Inferred from Reviewed Computational Analysis</td> <td>&nbsp;</td> <td>TAS:</td> <td> Traceable Author Statement</td> </tr>\
 <tr> <td>NR:</td><td> Not Recorded</td> </tr>\
</table>\
<p>\
See the <a href="http://www.geneontology.org/GO.evidence.shtml">GO website for more details</a>

<commit_msg>removed obsolete field, updated to gene.primaryIdentifier<commit_after># from so_defs file

AntisensePrimaryTranscript=The reverse complement of the primary transcript.
AntisenseRNA=Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
ARS=A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
Assembly=A sequence of nucleotides  that has been algorithmically derived from an alignment of two or more different sequences.
AssemblyComponent=A region of sequence which may be used to manufacture a longer assembled, sequence. 
Attenuator=A sequence segment located between the promoter and a structural gene that causes partial termination of transcription.
AutocatalyticallySplicedIntron=A self spliced intron.
BindingSite=A region on the surface of a molecule that may interact with another molecule.
BranchSite=A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
Cap=A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
CDNAMatch=A match against cDNA sequence.
CDS=A contiguous RNA sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
Centromere=A region of chromosome where the spindle fibres attach during mitosis and meiosis.
ChromosomalDeletion=An incomplete chromosome.
Chromosome=Structural unit composed of long DNA molecule. 
Clip=Part of the primary transcript that is clipped off during processing.
Clone=A piece of DNA that has been inserted in a vector so that it can be propagated in E. coli or some other organism.
CloneEnd=The end of the clone insert.
CloneStart=The start of the clone insert.
Codon=A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together signify a unique amino acid or the termination of translation. 
ComplexSubstitution=When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.
Contig=A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unknown/unavailable bases.
CpGIsland=Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
CRM=A regulatory region where more than 1 transcription factor binding site together are regulatorily active.
CrossGenomeMatch=A nucleotide match against a sequence from another organism.
DatabankEntry=The sequence referred to by an entry in a databank such as GenBank or UniProt.
DecayedExon=A non-functional descendent of an exon.
Deletion=The sequence that is deleted.
DeletionJunction=The space between two bases in a sequence which marks the position where a deletion has occurred.
DirectRepeat=A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.
DispersedRepeat=A repeat that is located at dispersed sites in the genome.
Enhancer=A cis-acting sequence that increases the utilisation of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
EnzymaticRNA=A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
EST=Expressed Sequence Tag: The sequence of a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
ESTMatch=A match against an EST sequence.
Exon=A region of the genome that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205).
ExonJunction=The boundary between two exons in a processed transcript.
ExperimentalResultRegion=A region of sequence implicated in an experimental result.
ExpressedSequenceMatch=A match to an EST or cDNA sequence.
FivePrimeUTR=A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
FlankingRegion=The DNA sequences extending on either side of a specific locus.
Gene="Gene" is an abstract term used to describe a collection of transcripts and related regulatory features.
GeneGroup=A collection of related genes.
GenePart=A part of a gene.
GoldenPath=A set of subregions selected from sequence contigs which when concatenated form a non-redundant linear sequence.
GoldenPathFragment=One of the pieces of sequence that make up a golden path.
GroupIIIntron=Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
GroupIIntron=Group I catalytic introns are large self-splicing ribozymes. They catalyse their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.
GuideRNA=short 3'-uridylated RNA that can form a perfect duplex (except for the oligoU tail (SO:0000609)) with a stretch of mature edited mRNA.
HammerheadRibozyme=A small catalytic RNA motif that catalyses self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs. 
Insertion=A region of sequence identified as having been inserted.
InsertionSite=The site where an insertion occurred.
IntegratedVirus=A viral sequence which has integrated into the host genome.
IntergenicRegion=The region between two known genes.
Intron=A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
Inversion=A continuous nucleotide sequence is inverted in the same position.
InvertedRepeat=The sequence is complementarily repeated on  the opposite strand. Example: GCTGA-----TCAGC.
Junction=A junction refers to an interbase location of zero in a sequence.
LocatedSequenceFeature=A biological feature that can be attributed to a region of biological sequence.
Match=A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
MatchPart=A part of a match, for example an HSP from BLAST isa match_part.
MatchSet=A collection of match parts
MaturePeptide=The coding sequence for the mature or final peptide or protein product following post-translational modification.
MethylatedA=A methylated adenine.
MethylatedBaseFeature=A nucleotide modified by methylation.
MethylatedC=A methylated deoxy-cytosine.
Microsatellite=A very short unit sequence of DNA (2 to 4 bp) that is repeated multiple times in tandem.
Minisatellite=A repetitive sequence spanning 500 to 20,000 base pairs (a repeat unit is 5 - 30 base pairs).
MiRNA=Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. miRNAs are produced from precursor molecules (SO:0000647) that can form  local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA  molecule accumulates from one arm of a hairpin-precursor molecule. miRNAs  may trigger the cleavage of their target molecules or act as translational repressors.
ModifiedBaseSite=A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U.
MRNA=The intermediate molecule between DNA and protein.
NcRNA=An mRNA sequence that does not encode for a protein rather the RNA molecule is the gene product.
NcPrimaryTranscript=A primary transcript that is never translated into a protein.
NucleaseSensitiveSite=A region of nucleotide sequence targeting by a nuclease enzyme.
NucleotideMatch=A match against a nucleotide sequence.
NucleotideMotif=A region of nucleotide sequence  corresponding to a known motif.
Oligo=A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
Operon=A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
ORF=A nucleic acid sequence that, when read as sequential triplets, has the potential of encoding a sequential string of amino acids.
OriginOfReplication=The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
PCRProduct=A region amplified by a PCR reaction.
PointMutation=A mutation event where a single DNA nucleotide changes into another nucleotide.
PolyASequence=Sequence of about 100 nucleotides of A at the 3' end of most eukaryotic mRNAs.
PolyASignalSequence=The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
PolyASite=The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation.
Polypeptide=A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
PolypeptideDomain=A region of a single polypeptide chain  that folds into an independent unit and exhibits biological activity. A  polypeptide chain may have multiple domains.
PolypyrimidineTract=The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
PossibleAssemblyError=A region of sequence where there may have been an error in the assembly.
PossibleBaseCallError=A region of sequence where the validity of the base calling is questionable.
PrecursorMiRNA=A miRNA transcript that has not been diced.
PrecursorRasiRNA=A rasiRNA transcript that has not been diced.
PrecursorSiRNA=A siRNA transcript that has not been diced.
PrimaryTranscript=The primary (initial, unprocessed) transcript; includes five_prime_clip (SO:0000555), five_prime_untranslated_region (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188) and three_prime_ untranslated_region (three_prime_UTR), and three_prime_clip (SO:0000557).
Primer=A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase.
ProbeSet=A set of probes which can be mapped to Genes.  For example, the Affymetrix Drosophila genome 2.0 array set.
ProcessedTranscript=A transcript which has undergone processing. The processing may include intron removal, 5' capping and polyadenlyation.
Promoter=The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
ProteinCodingPrimaryTranscript=A primary transcript that, at least in part, encodes one or more proteins.
ProteinMatch=A match against a protein sequence.
Pseudogene=A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). On occasion a pseudogene is functional as a consequence being "captured" by a non-paralogous gene, it is then known as a "captured_pseudogene" (SO:0100042). definition_reference:
PseudogenicRegion=A non-functional descendent of a functional entity.
RasiRNA=A small, 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
Read=A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
ReadPair=A pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
Reagent=A sequence used in experiment.
Region=Contiguous sequence.
RegulatoryRegion=A DNA sequence that controls the expression of a gene.
Regulon=A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.
Remark=A comment about the sequence.
RepeatFamily=A group of characterised repeat sequences.
RepeatRegion=A region of sequence containing one or more repeat sequences.
RestrictionEnzymeCutSite=A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA. 
RestrictionFragment=Any of the individual polynucleotide sequences produced by digestion of DNA with a restriction endonuclease.
RFLPFragment=A  polymorphism detectable by the size differences in DNA fragments generated by a restriction enzyme.
RibosomeEntrySite=Region in 5' UTR where ribosome assembles on mRNA.
Ribozyme=An RNA with catalytic activity.
RNAiReagent=A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
RNAiResult=The result from an RNAi screen. 
RNaseMRPRNA=The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
RNasePRNA=The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5 prime  ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
RRNA=RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
RRNA18S=18S_rRNA -A large polynucleotide which functions as a part of the small subunit of the ribosome
RRNA28S=A component of the large ribosomal subunit.
RRNA58S=5.8S ribosomal RNA (5.8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5.8S rRNA is also found in archaea.
RRNA5S=5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilises 5S rRNA until it is required for transcription.
SAGETag=A short diagnostic sequence tag,  serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
ScRNA=Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote. 
SequenceDifference=A region where the sequences differs from that of a specified sequence.
SequenceVariant=A region of sequence where variation has been observed.
SignalPeptide=The sequence  for an N-terminal domain of a secreted protein; this domain is involved in  attaching nascent polypeptide to the membrane leader sequence.
Silencer=Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes.
SiRNA=Small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. sRNAs trigger the cleavage of their target molecules.
SmallRegulatoryNcRNA=A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
SnoRNA=Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed, the box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localisation, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.
SNP=SNPs are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist in normal individuals in some population(s), wherein the least frequent allele has an abundance of 1% or greater.   
SnRNA=Small non-coding RNA in the nucleoplasm.
SpliceosomalIntron=An intron which is spliced by the spliceosome.
SpliceAcceptor=The junction between the 3 prime end of an intron and the following exon.
SpliceDonor=The junction between the 3 prime end of an exon and the following intron.
SpliceEnhancer=Region of a transcript that regulates splicing.
SpliceSite=The position where intron is excised.
SRPRNA=The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilises helix 8 for SRP54 binding.
StRNA=Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in  C. elegans.
STS=Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
Substitution=Any change in genomic DNA caused by a single event.
Supercontig=One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
SyntenicRegion=A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.
Tag=A nucleotide sequence that may be used to identify a  larger sequence.
TandemRepeat=Two or more adjacent copies of a DNA sequence.
TelomeraseRNA=The RNA component of telomerase, a reverse transcriptase that synthesises telomeric DNA.
Telomere=A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end,
Terminator=The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
TFBindingSite=A region of a molecule that binds to a transcription factor.
TFmodule=A regulatory region where more than 1 transcription factor binding site together are regulatorily active.
ThreePrimeUTR=A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
TilingPath=A set of regions which overlap with minimal polymorphism to form a linear sequence.
TilingPathFragment=A piece of sequence that makes up a tiling_path (SO:0000472.).
TmRNA=tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. tmRNAs have been identified in eubacteria and some chloroplasts but are absent from archaeal and eukaryote nuclear genomes.
Transcript=An RNA synthesised on a DNA or RNA template by an RNA polymerase.
TranscriptionEndSite=The region where transcription ends.
TranscriptionStartSite=The region where transcription begins.
TranslatedNucleotideMatch= A match against a translated sequence.
TransposableElement=A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
TransposableElementGene=A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
TransposableElementInsertionSite=The site in a genome where a transposable_element has inserted.
TransSpliceAcceptorSite=The process that produces mature transcripts by combining exons of independent pre-mRNA molecules. The acceptor site lies on the 3' of these molecules
TRNA=Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. tRNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). tRNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
U11SnRNA=U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
U12SnRNA=The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
U14SnRNA=U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
U1SnRNA=U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
U2SnRNA=U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
U4atacSnRNA=An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
U4SnRNA=U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to re-fold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
U5SnRNA=U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
U6atacSnRNA=U6atac_snRNA -An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
U6SnRNA=U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
UTR=Messenger RNA sequences that are untranslated and lie five prime and three prime to sequences which are translated.
VaultRNA=A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
VirtualSequence=A continuous piece of sequence similar to the 'virtual contig' concept of Ensembl.
YRNA=Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.



# Additional FlyMine-specific definitions
AGambiaeLifeCycle=Result from an Anopheles gambiae microarray experiment.
Amplicon=A piece of DNA that has been synthesised using amplification techniques.
Analysis=The description of a computational algorithm or experimental procedure.
AnalysisResult=The result of a computational algorithm or an experimental procedure that provides evidence for the existence of a piece of data.
AnatomyTerm=A structured controlled vocabulary term of the anatomy of Drosophila melanogaster, used, for example, for the description of phenotypes and where a gene is expressed.
Annotation=Links the BioProperties of BioEntities with the evidence for that BioProperty.
ArtificialDeletion=A nucleic acid sequence that is deleted artificially in the genome as opposed to being deleted naturally.
Author=The author of a publication.
BAC=Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host
BioEntity=The BioEntity class is the parent for more specialised classes of biological entities, such as Gene, Transcript etc.
BioProperty=Biological properties that have been assigned to BioEntities, such as GO annotation and phenotypes.
BlastMatch=A region of sequence, aligned to another sequence with some statistical significance, using the BLAST algorithm.
CDNAClone=Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
ChromosomeArm=A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere
ChromosomeBand=A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
Chunk=In order to provide access to the sequence of Anopheles gambiae and to facilitate annotation, scaffolds are treated as 'clones' in the Ensembl databases, and the larger scaffolds have been divided into chunks of approximately 25 kb.
Comment=A comment or description about a biological object (BioEntity).
CompositeSequence=A set of reporters used collectively to measure an expression of a particular gene, exon, or splice-variant.
ComputationalAnalysis=The description of a computational algorithm.
ComputationalResult=The result of a computational algorithm.
Database=An external database.
DataSet=A set of results or data from a data source.
DataSource=The origin of imported data.
Disease=Objects of this class are contain disease descriptions from the <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM">OMIM database</a>
ESTCluster= Set of joined ESTs.
Evidence=Provides evidence for a Relation, BioEntity or Annotation. The evidence could be a publication, external database or experimental or computational result.
Experiment=The description of an experimental procedure.
ExperimentalResult=The result of an experimental procedure.
FlyAtlasResult=A result from the FlyAtlas microarray project.
ForwardPrimer=A single stranded oligo used for polymerase chain reaction.
GenomeRegion=Continuous genomic sequence.
GOAnnotation=Objects of class GOAnnotation hold the Gene Ontology annotation for a gene.
GOEvidence=An evidence assigned by a GO annotator.
GOEvidenceCode=A three-letter code that indicates how annotation to a particular GO term is supported. These evidence codes correspond to broad categories of experimental or other support. 
GOTerm=A term from the Gene Ontology.
Group=Chromosome groups of Apis mellifera were assembled by joining scaffolds.
Homologue=Gene with common ancestry. A homologue can be an orthologue (genes separated by the event of speciation) or paralogue (genes separated by the event of genetic duplication).
InfoSource=The source of published information, either a publication or an external database.
InterMineObject=The parent class of all other classes in the database.
InterproEvidence=Extra evidence for InterPro objects.
Location=The location of one BioEntity on another.
Marker=A short sequence whose placement on the genome is known.
MicroArrayAssay=A single assay of a microarray experiment involving samples at particular conditions against a particular microarray chip. 
MicroArrayExperiment=A microarray experiment comprising multiple assays.
MicroarrayOligo=A gene-specific oligonucleotide designed for use in a microarray experiment.
MicroArrayResult=Numerical result for one sequence/sample pair in a particular microarray assay or derived from multiple assays.
ModelledProteinStructure=The three-dimensional conformation of a protein, as predicted by computational analysis.
Motif=A sequence motif is a short region of biological interest.
NuclearDNA=DNA that can be found in the nucleus of a cell.
Ontology=A controlled vocabulary.
OntologyRelation=The relationship between two terms in an ontology.
OntologyTerm=A term within an ontology.
OntologyTermSynonym=A synonym for a term from an ontology - an alternative name or symbol for a term.
Organism=A living thing.
Orthologue=Orthologues are equivalent genes in different species that evolved from a common ancestor by speciation.
OverlapRelation=Description of a pair of genome annotation features that have overlapping locations on a chromosome.
Paralogue=Paralogues are genes from the same homologous super-family found in another part of the genome of a particular taxon. Paralogues are the result of gene duplication.
PartialLocation=The location of part of a BioEntity on another.
Pathway=Molecular interaction network.
Phenotype=The observable characteristics of an organism. The expression of gene alleles (genotype) as an observable physical or biochemical trait.
Protein=One or more polypeptides which may, or may not, be covalently bonded, and which assume a native secondary and tertiary structure.
ProteinBindingSite=A region of a molecule that binds to a protein.
ProteinDomain=A region of a protein that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
ProteinFamily=A group of characterised protein sequences.
ProteinInteraction=A relation between two proteins which have been shown to be related through a physical interaction.
ProteinInteractionExperiment=The description of a particular protein interaction experiment.
ProteinInteractionRegion= The region of a protein molecule that binds to another protein molecule.
ProteinInteractionTerm=A term from the PSI-MI protein interaction ontology.
ProteinInteractor=A term for a protein involved in a protein interaction.
ProteinRegion=Amino acid sequence of part of a protein.
ProteinStructure=The three-dimensional conformation of a protein.
ProteinStructureExperiment=The type of experiment that was done to determine a protein structure.
Protocol=Documentation of the set of steps taken in a procedure.
Publication=A journal article, book etc.
RankedRelation=A relation that is part of an ordered set of relations. eg. the relationship between transcripts and exons.
Relation=Any relationship between two BioEntities. A relation object has a subject BioEntity and an object BioEntity.
Reporter=The nucleotide sequence present in a particular location on the array
ReversePrimer=A single stranded oligo used for polymerase chain reaction.
RNAiExperiment=The description of a particular RNAi experiment.
RNAiPhenotype=the phenotype of an RNA interference experiment.
RNAiResult=The result from an RNAi screen. This can be either a defined phenotype as a result from an in vivo screen (RNAiPhenotype) or a result from a screen done in cell culture (RNAiScreenHit).
RNAiScreen=A large-scale RNA interference experiment.
RNAiScreenHit=One experimental result from an RNAi screen (not necessarily a defined phenotype). Currently this is a result from one of the D. melanogaster RNAi screens done in cell-culture.
Sample=Description of the source of biological material. Can include information on such properties as species, developmental stage, organism part, gender and cell type.
SampleCharacteristic=Description of some characteristic (type and value) of a sample.
Scaffold=Larger sequence contigs that result from the assembly of shorter (often whole genome shotgun, WGS) sequencing reads which could not yet be assembled into chromosomes. Generally, more genome sequencing, narrowing of gaps and establishment of a tiling path is necessary before a chromosome assembly can be established.
Sequence=The order of building blocks in biological macromolecules like DNA, RNA, protein and polysaccharides.
SimpleRelation=A simple relationship between two BioEntities.
SymmetricalRelation=A relationship between two BioEntities that doesn't have direction - all objects are related to each other in the same way.
Synonym=Another name by which a BioEntity is known.
TilingPathSpan=A tiling path is a set of regions which overlap with minimal polymorphism to form a linear sequence. A TilingPathSpan starts at the initiation codon of one gene and ends at the initiation codon of a neighbouring gene or at a transposable element.
Translation=A possible translation of (part of) a gene that differs from the amino acid sequence found in the corresponding wild-type protein.
Treatment=A treatment is the process or action applied to a particular sample.
TreatmentParameter=A variable within the treatment.
UniProtFeature=A region or site of interest in a protein sequence (source: UniProt). Examples: post-translational modifications, binding sites, enzyme active sites, local secondary structures.
Vector=A DNA molecule that can be used to transfer DNA molecules between organisms.






# Class field descriptions

Gene.secondaryIdentifier=Any identifier, other than the main organism genome database identifier, which \
is commonly used to identify a gene (for example, the Drosophila CG identifier). See 'Synonyms' \
for other gene names and identifiers for this gene.<p>\

Gene.primaryIdentifier=The main identifier used by the organisms main genome database. \
For example, the FBgn identifier assigned by FlyBase or the WBGene identifier assigned by WormBase. \
See 'Synonyms' for other gene names and identifiers for this gene.<p>\

Gene.name=The gene symbol or common name. For most organisms this will be an officially assigned \
symbol/name (for example, the FlyBase gene symbol or the CGC-approved gene name for C. elegans). \
See 'Synonyms' for other gene names and identifiers for this gene.<p>\

Protein.primaryAccession=UniProt primary accession. See 'Synonyms' for other names and identifiers \
for this protein.
Protein.identifier=UniProt entry name (for example 18C_DROME). See 'Synonyms' for other names and \
identifiers for this protein.

Gene.allGoAnnotation=For a particular GO term, this provides that GO term and all the parent terms for that GO term.

Gene.length=Genomic length of the gene, i.e. sequences of all introns and exons.

Homologue.type=A homologue can be either an orthologue (related to the gene by the event of speciation and likely to be functionally related) or an inparalogue (related to the gene by a duplication event after a speciation of interest).

Homologue.inParanoidScore=The inparanoid program calculates orthologue \
and inparalogue clusters, pairwise between two organisms, by first \
finding the best recipricol blast match for each gene. This becomes \
the seed-orthologue to which inparalogues are clustered. Each member \
in the cluster receives an inparalog score which reflects the distance \ 
to the seed-orthologue. A score of 1.0 means there is identical \
distance to the seed orthologue (and so all orthologues in the cluster \
will have an inparanoid score of 1.0). Each inparalogue in the cluster \
will have a score less than one which reflects how similar it is to \
the seed orthologue.

Homologue.bootstrapScore=the confidence that this ortholog pair \
are true orthologues. (This is estimated by sampling how often the \
pair is found as recipricolly best matches by a bootstrapping \
procedure applied to the original Blast alignment).

Homologue.homologueBootstrapScore=the confidence that this ortholog pair \
are true orthologues. (This is estimated by sampling how often the \
pair is found as recipricolly best matches by a bootstrapping \
procedure applied to the original Blast alignment).

Homologue.clusterName=The inparanoid program calculates orthologue and \
inparalogue clusters, pairwise between two organisms, by first finding \
the best recipricol blast match for each gene. This becomes the \
seed-orthologue to which inparalogues are clustered. Each cluster can be identified by a unique cluster name.

FlyAtlasResult.affyCall=Reflects an up- or down-regulation (or no change at all) compared to the whole fly.

FlyAtlasResult.enrichment=This factor tells you how much higher the signal is in a particular tissue than in the whole fly, i.e. whether the gene is tissue-specific. 

FlyAtlasResult.MRNASignal=Abundance of the mRNA. FlyAtlas considers values over 100 as being abundant, and anything over 1000 as remarkable.

FlyAtlasResult.MRNASignalSEM= The SEM value tells you how consistent or variable the MRNASignal is.

FlyAtlasResult.presentCall=How many of the four arrays for each sample actually gave a detectable expression, according to Affymetrix's GCOS software. 

RNAiScreenHit.maxOffTargetOverlaps=The maximum continuous sequence overlap of potential off-target(s).

RNAiScreenHit.numOffTargets=The number of potential off-targets based on sequence matches: at least one length of 19 bp or more with matching sequence of 19 bp or more of this amplicon.

GOAnnotation.evidenceCode=Every GO annotation must indicate the type of evidence that supports it. \
The possibilities are:<p>\
<table>\
 <tr> <td>IC:</td><td> Inferred by Curator</td>              <td>&nbsp;</td> <td>IDA:</td> <td> Inferred from Direct Assay </td> </tr>\
 <tr> <td>IEA:</td><td> Inferred from Electronic Annotation</td>      <td>&nbsp;</td> <td>IEP:</td> <td> Inferred from Expression Pattern</td> </tr>\
 <tr> <td>IGI:</td><td> Inferred from Genetic Interaction</td>       <td>&nbsp;</td> <td>IMP:</td> <td> Inferred from Mutant Phenotype</td> </tr>\
 <tr> <td>IPI:</td><td> Inferred from Physical Interaction</td>      <td>&nbsp;</td> <td>ISS:</td> <td> Inferred from Sequence or Structural Similarity</td> </tr>\
 <tr> <td>NAS:</td><td> Non-traceable Author Statement</td>        <td>&nbsp;</td> <td>ND:</td> <td> No biological Data available</td> </tr>\
 <tr> <td>RCA:</td><td> Inferred from Reviewed Computational Analysis</td> <td>&nbsp;</td> <td>TAS:</td> <td> Traceable Author Statement</td> </tr>\
 <tr> <td>NR:</td><td> Not Recorded</td> </tr>\
</table>\
<p>\
See the <a href="http://www.geneontology.org/GO.evidence.shtml">GO website for more details</a>


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